Transcription biomarkers of biological responses and methods of use

ABSTRACT

This invention provides transcription regulatory control sequences, the activity of which function as biomarkers for a variety of biological responses. This invention also provides expression constructs in which a biomarker transcription regulatory sequence is operably linked with a sequence for a reporter. Cells that comprise these expression constructs can be used in assays to identify conditions that modulate activity of the biological response.

REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.12/586,131, filed Sep. 16, 2009, the contents of which are incorporatedherein by reference in their entirety.

SEQUENCE LISTING

A .txt file containing a Sequence Listing is filed with this applicationin lieu of a paper copy. The .txt file serves both as the SequenceListing and as the Computer Readable Form. The .txt file has thefollowing properties:

-   -   File Name: 1003-004-DIV-SL    -   File Size: 2.5 MB    -   Created: 2014-07-13    -   Other Information: ASCII text file generated by script execution        in Darwin Kernel of Unix (Mac OS 10.4.2); DOS compatible        new-line characters (ASCII\015\012) interpreted correctly in        MS-DOS, MS-Windows, Unix and Mac.

BACKGROUND OF THE INVENTION

Reporter constructs including an expression control sequence operablylinked with a reporter sequence are widely used in biology to test forthe activity of the expression control sequence under selectedconditions. Typically, such constructs are used to test for theexpression of the gene normally under transcriptional control of thecontrol sequence. Such constructs have many uses. They can be used, forexample, to monitor gene expression during cellular responses tosignaling cascades. They also are useful in drug development assays. Indrug development, the induction or suppression of expression of a geneby a drug candidate may be a desired or undesired event. In such assays,a cell that contains an expression construct comprising a controlsequence for the gene of interest is contacted with a drug candidate andthe expression of the reporter is monitored. Compositions that elicit anundesirable result may be eliminated from further testing.Alternatively, compositions that elicit a desired result may be subjectto further testing.

In this age of systems biology, investigators may wish to study theactivity of many genes in a biological response or pathway, or toidentify compositions that modulate the activity of a biologicalresponse. Biological responses are characterized by the induction orsuppression of many genes. Biological responses of interest include, forexample, (1) the hypoxia response, (2) the response to estrogens; (3)the response to androgens; (4) the response mediated by the p53 protein;(5) the response to inhibitors or activators of cholesterolbiosynthesis; (6) the interferon-mediated response; (7) theCREB-mediated response; (8) the response to glucocorticoids; (9) thePPAR-mediated response; (10) the RAR-mediated response; (11) theinflammation response induced by TNFa; (12) the heat shock response; and(13) the serum response.

Trinklein et al. have described a library that contains transcriptionregulatory sequences for thousands of genes in the genome and that areassociated with various pathways. See, e.g., U.S. patent publications2007-0161031 and 2009-0018031.

SUMMARY OF THE INVENTION

In one aspect this invention provides an expression construct comprisinga transcriptional regulatory sequence operatively linked with aheterologous sequence encoding a reporter, wherein the transcriptionregulatory sequence is one of a gene of Table 1. In one aspect thisinvention provides a collection comprising a plurality of expressionconstructs, each expression construct comprising a transcriptionalregulatory sequence operatively linked with a heterologous sequenceencoding a reporter, wherein at least 20% of the expression constructsin the collection each comprise a transcription regulatory sequence of adifferent gene of Table 1. In certain embodiments, the transcriptionregulatory sequences include at least a fragment of a sequence selectedfrom SEQ ID NO: 1 to SEQ ID NO. 174. In other embodiments, thetranscription regulatory sequences include at least a fragment of asequence selected from SEQ ID NO: 175 to SEQ ID NO. 1619. In oneembodiment at least 20% of the expression constructs comprisetranscription regulatory sequences differently selected from the groupconsisting of: (i) any of SEQ ID NO:1 to SEQ ID NO: 174; (ii) a sequenceof at least 50 nucleotides having at least 90% sequence identity to asequence of (i); and (iii) a fragment of a sequence of (i). In anotherembodiment the transcription regulatory sequences of the different genesof Table 1 are biomarkers of the same biological response. In anotherembodiment the transcription regulatory sequences of the different genesof Table 1 comprise biomarkers of different biological responses. Forexample, the plurality of different biological response could be 2, atleast 2, 3, at least 3, no more than 3, 4, at least 4, no more than 4,5, at least 5, no more than 5, 6, at least 6, no more than 6, 7, atleast 7, no more than 7, 8, at least 8, no more than 8, 9, at least 9,no more than 9, 10, at least 10, no more than 10, 11, at least 11, nomore than 11, 12, at least 12 no more than 12, or 13 differentbiological responses selected from (1) the hypoxia response, (2) theresponse to estrogens; (3) the response to androgens; (4) the responsemediated by the p53 protein; (5) the response to inhibitors oractivators of cholesterol biosynthesis; (6) the interferon-mediatedresponse; (7) the CREB-mediated response; (8) the response toglucocorticoids; (9) the PPAR-mediated response; (10) the RAR-mediatedresponse; (11) the inflammation response induced by TNFa; (12) the heatshock response; and (13) the serum response In another embodiment thetranscription regulatory sequences of the different genes of Table 1comprise at least three biomarkers of each of a plurality differentbiological responses. In another embodiment the expression construct iscomprised in a plasmid, a virus, or a transposon vector. In anotherembodiment the expression construct is integrated into a chromosome in acell or maintained as a stable episomal vector. In another embodimentthe reporter is a light-emitting reporter, a fluorescent reporter or acolorimetric reporter. In another embodiment the heterologous sequenceencoding the reporter comprises a luciferase gene. In another embodimentthe collection comprises at least 10 and no more than 1000 differentexpression constructs. In another embodiment the collection comprises atleast 10 and no more than 100 different expression constructs. Inanother embodiment the collection comprises at least 10 and no more than50 different expression constructs. In another embodiment the collectioncomprises at least 50 and no more than 100 different expressionconstructs. In another embodiment each expression construct is comprisedin a different molecule. In another embodiment each recombinant nucleicacid molecule is comprised in different well of at least one microtiterplate. In another embodiment the transcription regulatory sequences ofthe collection consist of or consist essentially of transcriptionregulatory sequences of genes of Table 1, or those comprising all orpart of the sequences in the sequence listing, including those in Part Iand/or Part II.

In one aspect this invention provides a cell comprising an expressionconstruct comprising a transcriptional regulatory sequence operativelylinked with a heterologous sequence encoding a reporter, wherein thetranscription regulatory sequence is one of a gene of Table 1. Inanother aspect this invention provides a collection of a plurality ofcells comprising expression constructs, each expression constructcomprising a transcriptional regulatory sequence operatively linked witha heterologous sequence encoding a reporter, wherein at least 20% of theexpression constructs each comprise a transcription regulatory sequenceof a different gene of Table 1. In one embodiment each cell is comprisedin different well of at least one microtiter plate. In anotherembodiment the cells are human cells. In another embodiment the cellsare mammalian cells. In another embodiment at least one expressionconstruct is stably integrated into a chromosome wherein the expressionconstruct comprises a transcriptional regulatory sequence operativelylinked with a heterologous sequence encoding a reporter, wherein theexpression construct comprises a transcription regulatory sequence of agene of Table 1. In another embodiment the cells comprise a plurality ofdifferent expression constructs, each comprising a transcriptionregulatory sequence of a different gene of Table 1. In anotherembodiment each different expression construct is comprised in adifferent cell of the cell line. In another embodiment the transcriptionregulatory sequences of the collection consist of or consist essentiallyof transcription regulatory sequences of genes of Table 1, or thosecomprising all or part of the sequences in the sequence listing,including those in Part I and/or Part II.

In another aspect this invention provides a multicellular organism thatcontains at least one expression construct comprising a transcriptionalregulatory sequence operatively linked with a heterologous sequenceencoding a reporter, wherein the expression construct comprises atranscription regulatory sequence of a gene of Table 1. In oneembodiment the multicellular organism is selected from a plant, avertebrate and an invertebrate.

In another aspect this invention provides a device comprising aplurality of receptacles, wherein each receptacle comprises anexpression construct comprising a transcriptional regulatory sequenceoperatively linked with a heterologous sequence encoding a reporter,wherein at least 20% of the expression constructs each comprise atranscription regulatory sequence of a different gene of Table 1. In oneembodiment the device comprises at least one microtiter plate.

In another aspect this invention provides a device comprising aplurality of receptacles, wherein each receptacle contains at least onecell comprising an expression construct, each expression constructcomprising a transcriptional regulatory sequence operatively linked witha heterologous sequence encoding a reporter, wherein at least 20% of theexpression constructs each comprise a transcription regulatory sequenceof a different gene of Table 1. In one embodiment the device comprisesat least one microtiter plate.

In another aspect this invention provides a method comprising: a)exposing at least one cell to a test condition, wherein the at least onecell comprises at least one expression construct comprising atranscriptional regulatory sequence operatively linked with aheterologous sequence encoding a reporter, wherein the transcriptionregulatory sequence is a transcription regulatory sequence of a gene ofTable 1; b) measuring expression of the reporter; and c) correlating themeasurement with a biological response for which the transcriptionregulatory sequence is a biomarker. In one embodiment the method furthercomprises i) measuring the activity of the reporter in the absence ofthe test condition; ii) measuring the activity of the reporter in thepresence of the test condition; iii) measuring the difference or ratioof reporter activity between the cells exposed to the test condition andcells that were not; and iv) correlating the difference or ratio betweentreated and untreated measurements with a biological response. In oneembodiment the transcription regulatory sequence comprises a sequenceselected from the group consisting of: (i) any of SEQ ID NO:1 to SEQ IDNO: 174; (ii) a sequence of at least 50 nucleotides having at least 95%sequence identity to a sequence of (i); and (iii) a fragment of asequence of (i). In another embodiment the test condition is selectedfrom the group consisting of contacting the cell with a test compound,exposing the cell to an environmental condition and inducing orrepressing expression of one or more genes in the cell. In anotherembodiment the test condition comprises removing a compound from theculture media in which the cell grown. In another embodiment the testcondition comprises contacting the cell with a test compound selectedfrom: (1) a small organic molecule; (2) a nucleic acid derivative (e.g.,a small interfering RNA, micro RNA mimic or micro RNA inhibitor); and(3) an expression construct that contains an open reading frame of agene. In another embodiment the test condition comprises exposing thecell to an environmental condition selected from hyperthermia,hypothermia, hypoxia, osmotic stress, oxidative stress, radiation, orchanges in atmospheric conditions. In another embodiment each expressionconstruct is comprised in a different cell. In another embodiment the atleast one cell comprises a plurality of the expression constructs,wherein each expression construct comprises a transcription regulatorysequence of a different gene of Table 1, wherein the transcriptionregulatory sequences of the different genes are biomarkers of the samebiological response. In another embodiment the at least one cellcomprises a plurality of the expression constructs, wherein eachexpression construct comprises a transcription regulatory sequence of adifferent gene of Table 1, wherein the transcription regulatorysequences of the different genes are biomarkers of different biologicalresponses. In another embodiment the at least one cell comprises aplurality of the expression constructs, wherein each expressionconstruct comprises a transcription regulatory sequence of a differentgene of Table 1, wherein the transcription regulatory sequences of thedifferent genes comprise at least three different biomarkers of each ofa plurality different biological responses. In another embodiment thebiological responses are responses selected from (1) the hypoxiaresponse, (2) the response to estrogens; (3) the response to androgens;(4) the response mediated by the p53 protein; (5) the response toinhibitors or activators of cholesterol biosynthesis; (6) theinterferon-mediated response; (7) the CREB-mediated response; (8) theresponse to glucocorticoids; (9) the PPAR-mediated response; (10) theRAR-mediated response; (11) the inflammation response induced by TNFa;(12) the heat shock response; and (13) the serum response. In anotherembodiment the method comprises contacting the test compound with aplurality of sets of different cell types, wherein each expressionconstruct is comprised in each of the cell types. In another embodimentthe method further comprises exposing a control cell to the testcondition, wherein the control cell comprises an expression constructcomprising a control transcriptional regulatory sequence operativelylinked with a heterologous sequence encoding a reporter, wherein thecontrol transcriptional regulatory sequence is a transcriptionalregulatory sequence of a gene whose activity is not correlated with abiological response correlated with the activity of transcriptionalcontrol sequence of the gene of Table 1. In another embodiment theexpression construct is comprised in a plasmid, a virus, or anartificial chromosome vector or a transposon vector. In anotherembodiment the expression construct is integrated into a chromosome inthe cell or maintained as a stable episomal vector. In anotherembodiment the reporter is a light-emitting reporter, a fluorescentreporter or a colorimetric reporter. In another embodiment the reportercomprises luciferase. In another embodiment the method further comprisesexposing the cell to a condition that induces the biological responsefor which the transcription regulatory sequence is a biomarker. Inanother embodiment correlating comprises correlating a change inbiomarker activity with induction of the biological response. In anotherembodiment correlating comprises correlating a change in biomarkeractivity with inhibition of the biological response. In anotherembodiment the method further comprises inducing the biological responseand wherein correlating comprises correlating inhibition of thebiomarker with inhibition of the biological response. In anotherembodiment the method further comprises inhibiting the biologicalresponse and wherein correlating comprises correlating inhibition of thebiomarker with induction of the biological response.

In another aspect this invention provides a method comprising: a)exposing at least one cell to a test condition, wherein the at least onecell comprises at least one expression construct comprising atranscriptional regulatory sequence operatively linked with aheterologous sequence encoding a reporter, wherein the transcriptionregulatory sequence is a transcription regulatory sequence of a gene ofTable 1; b) measuring expression of the reporter; and if the measurementis at a target level; c) exposing at least one second cell to the testcondition, wherein the at least one second cell comprises at least oneexpression construct comprising a transcriptional regulatory sequenceoperatively linked with a heterologous sequence encoding a reporter,wherein the transcription regulatory sequence is a transcriptionregulatory sequence of a different gene of the same biological responseof Table 1; and; d) measuring expression of the reporter sequence in theat least one second cell. In one embodiment the method furthercomprises: e) correlating the measurement with the biological response.

In another aspect this invention provides a method of determiningwhether a test condition modulates a biological response. In oneembodiment the method comprises exposing a cell comprising an expressionconstruct of this invention to the test condition and determiningwhether test condition modulates the activity of the biomarker promoter,wherein modulation of the activity of the biomarker promoter indicatesthat that the test condition modulates the biological response for whichthe biomarker promoter is a biomarker. In another embodiment this methodcomprises exposing a cell comprising an expression construct of thisinvention to conditions that induce or repress the biological responsefor which the biomarker promoter is a biomarker; exposing the cell tothe test condition and determining whether the test condition modulatesthe activity of the biomarker promoter, wherein modulation of theactivity indicates that the test condition modulates the activity of thebiological response. The activity of the biomarker promoter can bepositively or negative correlated with the activity of the biologicalresponse. In the case of positive correlation, induction of thebiomarker promoter is correlated with induction of the response and/orrepression of the biomarker promoter is correlated with repression ofthe biological response. In the case of negative correlation, repressionof activity of the promoter is correlated with induction of thebiological response and induction of activity of the promoter iscorrelated with repression of the biological response.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1. presents Table 1 showing biomarkers for various biologicalresponses. The table is divided into Part I and Part II. Each Part isdivided into sections. Each major section (e.g., Section 1, Section 2,etc.) relates to a particular biological response. Part B of Table 1presents other biomarkers of biological responses, again divided intosub-sections grouped as “Section 1a”, “Section 2a”, etc. In certainembodiments, biomarkers for a biological response in Part I arepreferred to those in Part II, e.g., biomarkers in Part I, Section 1 maybe preferred to those in Part II, section 1a.

DETAILED DESCRIPTION OF THE INVENTION

1. Biomarkers

This invention provides nucleic acid molecules comprising transcriptionregulatory sequences for genes useful as biomarkers of a variety ofbiological responses or biological pathways. The genes and thebiological responses/pathways are identified in Table 1. Certaintranscription regulatory sequences of these genes also are identified inTable 1 and provided in the sequence listing. This invention alsoprovides expression constructs comprising biomarker transcriptioncontrol sequences, devices including them and methods of use. Thebiomarker transcription expression control sequences are useful, amongother things, for identifying test conditions that modulate activity ofthe biological response or pathway. Modulation includes changing theactivity of a pathway, including increasing and decreasing activity.

Biomarkers exhibit different activity or expression under differentconditions or states. A biomarker is differentially active or presentbetween states if the mean or median activity or expression level of thebiomarker in the different states is calculated to be statisticallysignificant. Common tests for statistical significance include, amongothers, t-test, ANOVA, Kruskal-Wallis, Wilcoxon, Mann-Whitney and oddsratio. As such, the activity of a biomarker is correlated with a stateand the biomarker is useful in classification algorithms to classify anentity as belonging to one or another category. In the present context,activity of a biomarker expression control sequence in a cell indicateswhether a biological response or pathway is active in the cell. Cellsthat contain expression constructs comprising a biomarker expressioncontrol sequence operatively linked to a reporter sequence can besubject to a test condition. Activity of the biomarker expressioncontrol sequence provides an indication of whether the test conditionelicits activity of the biological response or pathway for which thetranscription regulatory sequence is a biomarker. For example, a cellcomprising an expression construct of this invention can be exposed to adrug candidate to determine whether the drug candidate elicits orinhibits a desired or undesired response, or to an environmentalstimulus or condition to determine whether the stimulus or conditionelicits or inhibits the response.

2. Biological Responses and Pathways

Biological responses are often characterized by the change in expressionof sets of genes. A set of genes whose expression is activated (orturned oft) as part of the biological response is referred to as a“pathway.” One goal is to identify compounds that modulate or mimic abiological response, or activate or inhibit activity of genes in apathway. A number of genes have been identified that have promoterswhose activity is highly correlated with particular biologicalresponses. Therefore, promoters of these genes function as biomarkers ofthe biological response. The genes are identified in Table 1, along withspecific transcriptional regulatory sequences that were determined tofunction as biomarkers of the response. In general, a transcriptionalregulatory sequence functions as a biomarker if the induction ratio (theratio between activity with induction of the response and the activitywithout induction of the response) is at least 2, at least 4, at least10, at least 25 or at least 50.

Biomarkers have been identified for the following biological responses:(1) the hypoxia response, (2) the response to estrogens; (3) theresponse to androgens; (4) the response mediated by the p53 protein; (5)the response to inhibitors or activators of cholesterol biosynthesis;(6) the interferon-mediated response; (7) the CREB-mediated response;(8) the response to glucocorticoids; (9) the PPAR-mediated response;(10) the RAR-mediated response; (11) the inflammation response inducedby TNFa; (12) the heat shock response; and (13) the serum response.

This invention provides collections of these biomarker promoters,expression constructs in which they are operably linked with sequencesencoding reporters, cells that contain these expression constructs,devices that contain the expression constructs and methods of usingexpression constructs, in particular to determine whether any testcondition can modulate the activity of particular biological responses,based on its ability to regulate the activity of the biomarkerexpression control sequences.

A biological response biomarker is positively correlated with thebiological response if its activity is induced or activated when abiological response is active, or if its activity is repressed when thebiological response is repressed. A biological response biomarker isnegatively correlated with the biological response if its activity isrepressed when a biological response is active, or if its activity isinduced or activated when the biological response is repressed.

Identifying test conditions that induce or repress the activity ofbiomarker promoters is useful to evaluate test conditions, such as testcompositions, for the ability to induce or inhibit the biologicalresponse with which the biomarker activity is correlated. A testcondition that induces activity of a biological response biomarkerpromoter positively correlated with the response is presumed to inducethe biological response in full or in part, e.g., to cause a responsethat mimics the biological response, and its action is correlatedpositively with the biological response. A test condition that inhibitsactivity of a biological response biomarker promoter positivelycorrelated with the response when cells are exposed to conditions thatinduce the biological response is presumed to inhibit the biologicalresponse, e.g., to inhibit events correlated with the biologicalresponse, and its action is correlated negatively with the biologicalresponse.

Alternatively, a test condition that inhibits activity of a biologicalresponse biomarker promoter negatively correlated with the response ispresumed to induce the biological response in full or in part, e.g., tocause a response that mimics the biological response, and its action iscorrelated positively with the biological response. A test conditionthat induces activity of a biological response biomarker promoternegatively correlated with the response when cells are exposed toconditions that induce the biological response is presumed to inhibitthe biological response, e.g., to inhibit events correlated with thebiological response, and its action is correlated negatively with thebiological response.

A method for identifying a test condition that elicits a biologicalresponse can comprise providing a cell comprising an expressionconstruct comprising a biological response biomarker promoter operablylinked to a reporter gene and exposing the cell to a test condition. Theactivity of a biological response biomarker promoter in response to thetest condition can be measured. The measurement can be correlated withthe biological response. Conditions resulting in activity of a desiredcorrelation (e.g., induction of activity of a positively correlatedbiomarker, or inhibition of the activity a negatively correlatedbiomarker) can be identified as conditions that elicit the biologicalresponse.

A method for identifying a test condition that inhibits a biologicalresponse can comprise providing a cell comprising an expressionconstruct comprising a biological response biomarker promoter operablylinked to a reporter gene, exposing the cell to a condition that elicitsa biological response (or to a condition that induces expression of abiological response biomarker promoter) and exposing the cell to a testcondition. The activity of a biological response biomarker promoter inresponse to the test condition can be measured. The measurement can becorrelated with the biological response. Conditions resulting inactivity of a desired correlation (e.g., inhibition of the inducibleactivity of a positively correlated biomarker, or induction of activityof a negatively correlated biomarker) can be identified as conditionsthat inhibit the biological response.

In each situation, the test condition can be tested further. Forexample, the ability of the test condition to modulate activity of atleast one or a plurality of different biomarkers for the biologicalresponse can be tested. The activity of these promoters can becorrelated with the biological response. The test condition also can betested for the ability to modulate a different biological response thanthe one originally tested.

2.1 Biological Response to Hypoxia

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to hypoxia (“hypoxiaresponse biomarker promoter”). These hypoxia response biomarkerpromoters are identified in Table 1, section 1 and section 1a. Hypoxiaresponse biomarker promoters generally have inducible activities rangingfrom 2 to 10-fold typically in this assay. The conditions used to inducethe biological response to hypoxia included exposing cells to a 1%oxygen environment and 100 micromolar deferoxamine (DFO) for 24 hrs. Theexperimental conditions are set forth more completely in Example 1.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to low oxygen conditions. Low oxygenconditions induce the hypoxia response. One can use such a promoter inan assay to determine whether a test compound induces the hypoxiaresponse. This is done, for example, by exposing a cell containing anexpression construct comprising the transcription regulatory sequenceoperatively linked with a reporter sequence to a test compound. If thecompound induces activity of the promoter, this means the compoundinduces the hypoxia response. Also, one can use the promoter in an assayto determine whether a test compound inhibits the hypoxia response. Thisis done, for example, by exposing a cell containing the expressionconstruct to a condition that induces the hypoxia response (for example,exposing the cell to low oxygen conditions) and exposing the cell to thetest compound. If the compound inhibits the inducible activity of thepromoter, this means the compound inhibits the hypoxia response.

The biological response to hypoxia (or, “hypoxia response”) involves anumber of events at the phenotypic, cellular and molecular level. Theseevents include increasing the expression of genes involved in cellularrespiration and promotion of vascularization and oxygen uptake. Theactivity of hypoxia response biomarker promoters is, in turn, alsocorrelated with these events.

In certain situations it may be useful to induce a hypoxia response. Forexample, hypoxia occurs under ischemic conditions, e.g., heart disease,transient ischemic attack, cerebrovascular accident, rupturedarteriovenous malformation and peripheral artery occlusive disease.Under such conditions, cells and tissue can be damaged. For example, asubject can experience cell death in the ischemic area. Pharmaceuticaldrugs that induce hypoxia may provide protection in situations ofischemia-induced hypoxia.

In certain situations it may be useful to inhibit a hypoxia response.For example, tumor growth results in hypoxic conditions. Under suchconditions, it may be beneficial to block the hypoxia response in orderto slow or stop tumor growth. Pharmaceutical drugs that inhibit orprevent the results of tumor-induced hypoxia are useful in treating suchconditions.

Conditions can be tested for their ability to induce or inhibit thehypoxia response, as discussed above. Hypoxia conditions to which cellscan be exposed for these tests include, for example, exposure of cellsto an environment in which oxygen is present at no more than about 10%,no more than about 5%, no more than about 3%, no more than about 2%, nomore than about 1% or below about 1%. Furthermore, small moleculeinhibitors of the cells ability to make or use ATP also elicit thehypoxia response, e.g., or treating with deferoxamine (DFO) for 24 hrs.DFO is a known inhibitor of mitochondria and inducer of hypoxia. Also,cells can be exposed to any condition that induces expression of ahypoxia response biomarker promoter.

2.2 Biological Response to Estrogen (e.g., β-Estradiol)

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to estrogen(“estrogen response biomarker promoter”). These estrogen responsebiomarker promoters are identified in Table 1, section 2 and section 2a.The condition used to induce the biological response to estrogen wasexposing cells to a 10 nanomolar environment of β-estradiol for 24 hrs.The experimental conditions are set forth more completely in Example 2.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to estrogens. β-estradiol induces theestrogen receptor protein that regulates the estrogen response. One canuse such a promoter in an assay to determine whether a test compoundinduces the estrogen response. This is done, for example, by exposing acell containing an expression construct comprising the transcriptionregulatory sequence operatively linked with a reporter sequence to atest compound. If the compound induces activity of the promoter, thismeans the compound induces the estrogen response. Also, one can use thepromoter in an assay to determine whether a test compound inhibits theestrogen response. This is done, for example, by exposing a cellcontaining the expression construct to a condition that induces theestrogen response and exposing the cell to the test compound. If thecompound inhibits the inducible activity of the promoter, this means thecompound inhibits the estrogen response.

The biological response to estrogen (or, “estrogen response”) involves anumber of events at the cellular and molecular level. These eventsinclude cell proliferation and lipid metabolism. The activity ofestrogen response biomarker promoters is, in turn, also correlated withthese events.

In certain situations it is useful to elicit an estrogen response. Forexample, estrogens are administered as drugs in a variety of situations.In a form of hormone replacement therapy, estrogen is administered topen-menopausal and post-menopausal women to counter the effects ofdiminished estrogen levels, such as osteoperosis. The estrogen responsebiomarker promoters of this invention are useful in discovering andevaluating pharmaceutical drugs and other conditions for the ability toelicit an estrogen response.

Also, in certain situations it is desirable to inhibit an estrogenresponse. For example, certain cancers, e.g., certain breast cancers,are hormone receptor positive. That is, cancer cells grow faster in thepresence of estrogen. Drugs that lower the amount of estrogen, or thatinhibit the activity of estrogen, such as tamoxifen, are used to treatsuch cancers. The estrogen response biomarker promoters of thisinvention are useful in discovering and evaluating pharmaceutical drugsand other conditions for the ability to inhibit an estrogen response.

Furthermore, it is known than many environmental toxins and other smallmolecules can act as estrogen mimics Therefore, an estrogen responsebiomarker promoter can serve as a useful tool for establishing whichtoxins or other small molecules can serve as estrogen mimics by, forexample, exposing a recombinant cell of this invention to the compoundand determining whether it induces activity of an estrogen biomarkerpromoter.

Conditions can be tested for their ability to induce or inhibit theestrogen response, as discussed above. Estrogen conditions to whichcells can be exposed for these tests include, for example, exposure ofcells to an environment comprising an estrogen at a concentration ofleast 100 picomolar, at least 1 nM or at least 10 nM or at least 1 uM.Any estrogen can be used to induce this response. Also, cells can beexposed to any condition that induces expression of an estrogen responsebiomarker promoter.

2.3 Biological Response to Androgen (e.g., Methyltrienolone)

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to androgen(“androgen response biomarker promoter”). These androgen responsebiomarker promoters are identified in Table 1, section 3 and section 3a.The condition used to induce the biological response to androgen wasexposing cells to a 10 nanomolar environment of methyltrienolone (R1881)for 24 hrs. The experimental conditions are set forth more completely inExample 3.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to androgens. Methyltrienolone induces theandrogen receptor protein that regulates the androgen response. One canuse such a promoter in an assay to determine whether a test compoundinduces the androgen response. This is done, for example, by exposing acell containing an expression construct comprising the transcriptionregulatory sequence operatively linked with a reporter sequence to atest compound. If the compound induces activity of the promoter, thismeans the compound induces the androgen response. Also, one can use thepromoter in an assay to determine whether a test compound inhibits theandrogen response. This is done, for example, by exposing a cellcontaining the expression construct to a condition that induces theandrogen response and exposing the cell to the test compound. If thecompound inhibits the inducible activity of the promoter, this means thecompound inhibits the androgen response.

The biological response to androgen (or, “androgen response”) involves anumber of events at the cellular and molecular level. These eventsinclude regulating gene expression patterns that result in the formationof male secondary sex characteristics in vertebrates. The activity ofandrogen response biomarker promoters is, in turn, also correlated withthese events.

In certain situations it is useful to elicit an androgen response. Forexample, in a form of hormone replacement therapy, androgen isadministered to older men to counter the effects of diminished androgenlevels. The androgen response biomarker promoters of this invention areuseful in discovering and evaluating pharmaceutical drugs and otherconditions for the ability to elicit an androgen response.

Also, in certain situations it is desirable to inhibit an androgenresponse. For example, androgen ablation can be used as an effectivetherapy in prostate cancer. The androgen response biomarker promoters ofthis invention are useful in discovering and evaluating pharmaceuticaldrugs and other conditions for the ability to inhibit an androgenresponse.

Furthermore, it is known than many environmental toxins and other smallmolecules can act as androgen mimics Therefore, an androgen responsebiomarker promoter can serve as a useful tool for establishing whichtoxins or other small molecules can serve as androgen mimics.

Androgen conditions to which cells can be exposed for these testsinclude, for example, exposure of cells to an environment comprising anandrogen at a concentration of least 100 picomolar, at least 1 nM or atleast 10 nM. Androgens include natural and artificial androgens, such astestosterones, methyltrienolone, and others. Also, cells can be exposedto any condition that induces expression of an androgen responsebiomarker promoter.

2.4 Biological Response to p53 Activation

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to the activation ofthe p53 tumor suppressor protein (“p53 response biomarker promoter”).These p53 biomarker promoters are identified in Table 1, section 4 andsection 4a. The conditions used to induce the biological response to p53was exposing cells to a 10 micromolar environment of nutlin for 24 hrsor treatment with doxorubicin at 200 ng/mL final concentration. Theexperimental conditions are set forth more completely in Example 4.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to activators of p53. Nutlin induces thep53 protein by inhibiting the MDM2 protein that is responsible for thedegradation of the p53 protein. Doxorubicin is an antibiotic thatinteracts with DNA by intercalation. This in turn activates p53. One canuse such a promoter in an assay to determine whether a test compoundinduces the p53 response. This is done, for example, by exposing a cellcontaining an expression construct comprising the transcriptionregulatory sequence operatively linked with a reporter sequence to atest compound. If the compound induces activity of the promoter, thismeans the compound induces the p53 response. Also, one can use thepromoter in an assay to determine whether a test compound inhibits thep53 response. This is done, for example, by exposing a cell containingthe expression construct to a condition that induces the p53 responseand exposing the cell to the test compound. If the compound inhibits theinducible activity of the promoter, this means the compound inhibits thep53 response.

p53 is a master tumor suppressor gene that controls a number of criticalevents at the cellular and molecular level. The p53 protein is atranscription factor that directly binds to DNA and regulates theexpression of genes involved in the cell cycle, the DNA repair pathway,and can initiate apoptosis if DNA damage is irreparable. The activity ofp53-responsive biomarker promoters, in turn, also correlate with theseevents.

p53 is critical to proper functioning of cells. A large number ofcancers develop from cells that have inactivated the p53 protein. Thep53 response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to activate the p53 response. Test conditions that stimulatethe p53 response may be useful in treating cancer.

Conditions can be tested for their ability to induce or inhibit the p53response, as discussed above. Conditions to which cells can be exposedfor these tests include, for example, exposure of cells to anenvironment that induces DNA damage, apoptosis, or other disruptions tothe cell cycle. Also, cells can be exposed to any condition that inducesexpression of an p53 response biomarker promoter.

2.5 Biological Response to Cholesterol and Other Molecules that Modulatethe Cholesterol Biosynthesis Pathway

Several promoters have been identified, the activity of which arepositively or negatively correlated with the biological response to theactivity of the cholesterol biosynthesis pathway (“cholesterol biomarkerpromoter”). These cholesterol response biomarker promoters areidentified in Table 1, section 5 and section 5a. The conditions used toinduce the cholesterol response were exposing cells to a 1 micromolarenvironment of lovastatin for 24 hrs (negatively correlated withactivation of the pathway or positively correlated with inhibition ofthe pathway), U18666A at 1 micromolar for 24 hrs (negatively correlatedwith activation of the pathway or positively correlated with inhibitionof the pathway), or synthecol at 5 ug/mL for 24 hrs (positivelycorrelated with activation of the pathway). The experimental conditionsare set forth more completely in Example 5.

More specifically, transcription regulatory sequences have been foundthat are induced or repressed when the cholesterol biosynthesis iseither inhibited or induced. Lovastatin is a known inhibitor of theHMG-coA reductase protein that is a critical enzyme in the synthesis ofcholesterol. U18666A is a known inhibitor of intracellular cholesteroltransport. Synthecol is a synthetic form of cholesterol. One can usesuch a promoter in an assay to determine whether a test compound affectsthe cholesterol response. This is done, for example, by exposing a cellcontaining an expression construct comprising the transcriptionregulatory sequence operatively linked with a reporter sequence to atest compound. If the compound induces activity of biomarker promoterspositively correlated with inhibition of cholesterol biosynthesis(negatively correlated with cholesterol biosynthesis), this means thecompound inhibits activity of the cholesterol biosynthesis pathway. Ifthe compound induces activity of biomarker promoters positivelycorrelated with cholesterol biosynthesis this means it induces activityof the cholesterol biosynthesis pathway. Similarly, one can induce orrepress the cholesterol synthesis response and determine whether a testcondition has the opposite effect, e.g., repressing activity of abiomarker positively correlated with the response or inducing activityof a biomarker negatively correlated with the response.

The cholesterol biosynthesis pathway includes a number of events at thecellular and molecular level. These events include the sensing ofintracellular cholesterol in the endoplasmic reticulum by the SREBPprotein. SREBP is a transcription factor that directly binds DNA andregulates the transcription of the HMG-CoA reductase and LDL receptorgenes. The activity of cholesterol biomarker promoters is, in turn, alsocorrelated with these events.

In certain situations it is useful to inhibit cholesterol biosynthesisas high levels of cholesterol are strongly associated withcardiovascular disease. For example, statins are some of the most widelyprescribed drugs that inhibit the activity of HMG-CoA reductase, a keyenzyme in the cholesterol biosynthesis pathway. The cholesterolbiomarker promoters of this invention are useful in discovering andevaluating pharmaceutical drugs and other conditions for the ability toinhibit cholesterol biosynthesis.

Also, in certain situations it may be desirable to activate thecholesterol biosynthesis pathway. There are rare cases of individualsthat suffer from hypocholesterolemia, or abnormally low levels ofcholesterol. The cholesterol biomarker promoters of this invention areuseful in discovering and evaluating pharmaceutical drugs and otherconditions for the ability to activate cholesterol biosynthesis.

Conditions can be tested for their ability to induce or inhibit thecholesterol biosynthesis pathway, as discussed above. Conditions towhich cells can be exposed for these tests include, for example,exposure of cells to any condition that inhibits the production ofcholesterol or the uptake of cholesterol. Statins are examples ofcholesterol synthesis inhibitors. Also, cells can be exposed to anycondition that induces expression of a cholesterol response biomarkerpromoter.

2.6 Biological Response to Interferons

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to interferons(“interferon biomarker promoter”). These interferon response biomarkerpromoters are identified in Table 1, section 6 and section 6a. Theconditions used to induce the interferon response were exposing cells to500 units/mL of interferon alpha for 8 hrs, or interferon gamma at 100ng/mL for 8 hrs. The experimental conditions are set forth morecompletely in Example 6. Certain of these biomarkers are correlated withthe alpha and/or gamma interferon responses.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to interferons, e.g., interferon alpha orinterferon gamma. Interferon alpha and gamma induce aninterferon-mediated response. One can use such a promoter in an assay todetermine whether a test compound induces the interferon-mediatedresponse. This is done, for example, by exposing a cell containing anexpression construct comprising the transcription regulatory sequenceoperatively linked with a reporter sequence to a test compound. If thecompound induces activity of the promoter, this means the compoundinduces the interferon-mediated response. Also, one can use the promoterin an assay to determine whether a test compound inhibits theinterferon-mediated response. This is done, for example, by exposing acell containing the expression construct to a condition that induces theinterferon-mediated response (for example, exposing the cell tointerferon alpha) and exposing the cell to the test compound. If thecompound inhibits the inducible activity of the promoter, this means thecompound inhibits the interferon-mediated response.

The biological response to interferons includes a number of events atthe cellular and molecular level. Interferons are produced by a widevariety of cells and are key signaling molecules in the inflammationresponse and in response to the presence of double-stranded RNA viruses.Interferons assist the immune response by inhibiting viral replicationwithin host cells, activating natural killer cells and macrophages,increasing antigen presentation to lymphocytes, and inducing theresistance of host cells to viral infection. The STAT family oftranscription factors directly bind DNA and regulate the transcriptionof target genes in response to interferon signaling. The activity ofinterferon biomarker promoters is, in turn, also correlated with theseevents.

In certain situations it is useful to inhibit interferon activity. Forexample, inhibiting interferon activity may help in cases of acute orchronic inflammation. The interferon biomarker promoters of thisinvention are useful in discovering and evaluating pharmaceutical drugsand other conditions for the ability to inhibit interferon activity.

Also, in certain situations it may be desirable to activate interferonactivity. For example, interferons have antiviral and antioncogenicproperties and are used to treat viral infection and cancer. Theinterferon biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to activate interferon activity.

Conditions can be tested for their ability to induce or inhibitinterferon activity, as discussed above. Conditions to which cells canbe exposed for these tests include, for example, exposure of cells tointerferon alpha or interferon gamma, or any condition that inhibits oractivates the production of interferon proteins, such as a viralinfection. Also, cells can be exposed to any condition that inducesexpression of an interferon biomarker promoter.

2.7. CREB-Mediated Response and Cyclic AMP Signaling

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to cAMP or CREBsignaling (“CREB biomarker promoter”). These CREB response biomarkerpromoters are identified in Table 1, section 7 and section 7a. Theconditions used to induce the cholesterol response were exposing cellsto 20 micromolar of forskolin for 4 hrs, or phorbol 12-myristate13-acetate (PMA) at 100 nanomolar for 4 hrs. The experimental conditionsare set forth more completely in Example 7.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to conditions that activate the CREBsignaling cascade. Forskolin is a known activator of protein kinase Athat raises cellular cyclic AMP (cAMP) levels. The CREB protein is atranscription factor that is activated by protein kinase A and directlybinds DNA to activate target genes. PMA is a known activator of proteinkinase C that also activates the CREB signaling cascade. One can usesuch a promoter in an assay to determine whether a test compound inducesa CREB-mediated response. This is done, for example, by exposing a cellcontaining an expression construct comprising the transcriptionregulatory sequence operatively linked with a reporter sequence to atest compound. If the compound induces activity of the promoter, thismeans the compound induces a CREB-mediated response. Also, one can usethe promoter in an assay to determine whether a test compound inhibits aCREB-mediated response. This is done, for example, by exposing a cellcontaining the expression construct to a condition that induces aCREB-mediated response (for example, exposing the cell to forskolin) andexposing the cell to the test compound. If the compound inhibits theinducible activity of the promoter, this means the compound inhibits theCREB-mediated response.

The biological response to CREB-mediated cyclic AMP signaling includes anumber of events at the cellular and molecular level. cAMP is asecondary messenger used for intracellular signaling that ultimatelyactivates the CREB transcription factor. CREB-mediated cyclic AMPsignaling is involved in many biological functions including regulatingthe effects of glucagons and adrenaline. The activity of CREB biomarkerpromoters is, in turn, also correlated with these events.

In certain situations it may be useful to inhibit certain aspects ofCREB activity. For example, inhibiting CREB activity may help in casesof metabolic disorders or signaling through certain G-protein coupledreceptor (GPCR) pathways. The CREB biomarker promoters of this inventionare useful in discovering and evaluating pharmaceutical drugs and otherconditions for the ability to inhibit CREB activity.

Also, in certain situations it may be desirable to activate CREBactivity. For example, activating CREB activity may help in cases ofmetabolic disorders or signaling through certain GPCR pathways. The CREBbiomarker promoters of this invention are useful in discovering andevaluating pharmaceutical drugs and other conditions for the ability toactivate CREB activity.

Conditions can be tested for their ability to induce or inhibit CREBactivity, as discussed above. Conditions to which cells can be exposedfor these tests include, for example, exposure of cells to anyconditions that change cAMP levels within the cell, the stimulation ofany GPCR protein, or other ways of activating the CREB protein e.g.,exposing cells to biogenic amines, chemokines, or peptide hormones.Also, cells can be exposed to any condition that induces expression of aCREB biomarker promoter.

2.8. Glucocorticoid Response

Several promoters have been identified, the activity of each of which ispositively correlated

with the biological response to glucocorticoid receptor (GR) signaling(“GR biomarker promoter”). These GR response biomarker promoters areidentified in Table 1, section 8 and section 8a. The conditions used toinduce the GR response were exposing cells to 100 nanomolardexamethasone, 1 micromolar prednisone, and 1 micromolar cortisone, eachfor 4 hrs. The experimental conditions are set forth more completely inExample 8.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to conditions that induce the GR-mediatedresponse. Dexamethasone, prednisone, and cortisone are known ligands andactivators of the GR protein. GR is a ligand-mediated transcriptionfactor that binds directly to the DNA of target genes in the genome whenit is bound to an activating ligand. Dexamethasone and prednisone arealso potent anti-inflammatory therapeutic compounds. Activating GR withsynthetic ligands is known to inhibit the inflammatory response, and istherefore, GR is an important drug target. One can use such a promoterin an assay to determine whether a test compound induces a GR-mediatedresponse. This is done, for example, by exposing a cell containing anexpression construct comprising the transcription regulatory sequenceoperatively linked with a reporter sequence to a test compound. If thecompound induces activity of the promoter, this means the compoundinduces a GR-mediated response. Also, one can use the promoter in anassay to determine whether a test compound inhibits a GR-mediatedresponse. This is done, for example, by exposing a cell containing theexpression construct to a condition that induces a GR-mediated response(for example, exposing the cell to dexamethasone) and exposing the cellto the test compound. If the compound inhibits the inducible activity ofthe promoter, this means the compound inhibits the GR-mediated response.

The biological response to ligands for GR (or, “GR response”) involves anumber of events at the cellular and molecular level. These eventsinclude GR-mediated expression of genes controlling development,metabolism, and the immune response. The activity of GR responsebiomarker promoters is, in turn, also correlated with these events.

In certain situations it is useful to activate a GR response. ActivatingGR activity is known to have potent anti-inflammatory effects. The GRresponse biomarker promoters of this invention are useful in discoveringand evaluating pharmaceutical drugs and other conditions for the abilityto elicit a GR response.

Also, in certain situations it is desirable to inhibit a GR response.For example, inhibiting GR may help in cases of metabolic disorders. TheGR response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to inhibit a GR response.

Furthermore, it is known than many environmental toxins and other smallmolecules can act as synthetic mimics of GR ligands. Therefore, an GRresponse biomarker promoter can serve as a useful tool for establishingwhich toxins or other small molecules can serve as GR ligand mimics by,for example, exposing a recombinant cell of this invention to thecompound and determining whether it induces activity of an GR biomarkerpromoter.

Conditions can be tested for their ability to induce or inhibit the GRresponse, as discussed above. GR activating conditions to which cellscan be exposed for these tests include, for example, any compound orcondition that simulates GR binding to its natural ligands.

2.9. PPAR-Mediated Response

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to peroxisomeproliferator-activated receptor (PPAR) signaling (“PPAR biomarkerpromoter”). These PPAR response biomarker promoters are identified inTable 1, section 9 and section 9a. The conditions used to induce thePPAR response were exposing cells to PPAR alpha and 75 micromolar ofWY14643, PPAR gamma and 10 micromolar of ciglitazone, or PPAR delta and100 nanomolar of GW501516 for 24 hrs. The experimental conditions areset forth more completely in Example 9.

More specifically, transcription regulatory sequences have been foundthat are induced when the PPAR-mediated response is activated. WY14643,ciglitazone and GW501516 are known ligands and activators of the PPARalpha, gamma, and delta proteins, respectively. The PPAR family oftranscription factors is a family of ligand-mediated transcriptionfactors that binds directly to the DNA of target genes in the genomewhen it is bound to an activating ligand. One can use such a promoter inan assay to determine whether a test compound induces a PPAR-mediatedresponse. This is done, for example, by exposing a cell containing anexpression construct comprising the transcription regulatory sequenceoperatively linked with a reporter sequence to a test compound. If thecompound induces activity of the promoter, this means the compoundinduces a PPAR-mediated response. Also, one can use the promoter in anassay to determine whether a test compound inhibits a PPAR-mediatedresponse. This is done, for example, by exposing a cell containing theexpression construct to a condition that induces a PPAR-mediatedresponse (for example, exposing the cell to ciglitazone) and exposingthe cell to the test compound. If the compound inhibits the inducibleactivity of the promoter, this means the compound inhibits thePPAR-mediated response.

The biological response to ligands binding to and activating PPAR (or“PPAR response”) involves a number of events at the cellular andmolecular level. These events include PPAR-mediated expression of genesthat play essential roles in the regulation of cellular differentiation,development, lipid metabolism, and tumorigenesis in higher organisms.The activity of PPAR response biomarker promoters is, in turn, alsocorrelated with these events.

In certain situations it is useful to activate a PPAR response.Activating PPAR activity is known to have anti-diabetic effects. ThePPAR response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to elicit a PPAR response.

Also, in certain situations it is desirable to inhibit a PPAR response.For example, inhibiting PPAR may help in cases of metabolic disorders.The PPAR response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to inhibit a PPAR response.

Furthermore, it is known than many environmental toxins and other smallmolecules can act as synthetic mimics of PPAR ligands. Therefore, a PPARresponse biomarker promoter can serve as a useful tool for establishingwhich toxins or other small molecules can serve as PPAR ligand mimicsby, for example, exposing a recombinant cell of this invention to thecompound and determining whether it induces activity of an PPARbiomarker promoter.

Conditions can be tested for their ability to induce or inhibit the PPARresponse, as discussed above. PPAR activating conditions to which cellscan be exposed for these tests include, for example, any compound orcondition that simulates PPAR binding to its ligand binding domain.

2.10 RAR-Mediated Response

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to retinoic acidreceptor (RAR) signaling (“RAR biomarker promoter”). These RAR responsebiomarker promoters are identified in Table 1, section 10 and section10a. The conditions used to induce the RAR response was exposing cellsto the RAR beta protein and 100 nanomolar of adapalene for 24 hrs. Theexperimental conditions are set forth more completely in Example 10.

More specifically, transcription regulatory sequences have been foundthat are induced when upon activation of the RAR-mediated response.Adapalene is a known ligand and activator of the RAR beta protein. RARis a ligand-mediated transcription factor that binds directly to the DNAof target genes in the genome when it is bound to an activating ligand.One can use such a promoter in an assay to determine whether a testcompound induces a RAR-mediated response. This is done, for example, byexposing a cell containing an expression construct comprising thetranscription regulatory sequence operatively linked with a reportersequence to a test compound. If the compound induces activity of thepromoter, this means the compound induces a RAR-mediated response. Also,one can use the promoter in an assay to determine whether a testcompound inhibits a RAR-mediated response. This is done, for example, byexposing a cell containing the expression construct to a condition thatinduces a RAR-mediated response (for example, exposing the cell toadapalene) and exposing the cell to the test compound. If the compoundinhibits the inducible activity of the promoter, this means the compoundinhibits the RAR-mediated response.

The biological response to ligands binding to and activatin RAR (or,“RAR response”) involves a number of events at the cellular andmolecular level. These events include RAR-mediated expression of genesthat play essential roles in the regulation of cellular differentiationand development. The activity of RAR response biomarker promoters is, inturn, also correlated with these events.

In certain situations it is useful to activate a RAR response.Activating RAR activity through various retinoids is known to play rolesin vision, cell proliferation, bone growth, and immune function. The RARresponse biomarker promoters of this invention are useful in discoveringand evaluating pharmaceutical drugs and other conditions for the abilityto elicit a RAR response.

Also, in certain situations it is desirable to inhibit a RAR response.For example, inhibiting RAR may help in cases of carcinogenesis or tumorgrowth. The RAR response biomarker promoters of this invention areuseful in discovering and evaluating pharmaceutical drugs and otherconditions for the ability to inhibit a RAR response.

Furthermore, it is known than many environmental toxins and other smallmolecules can act as synthetic mimics of retinoids or other RAR ligands.Therefore, a RAR response biomarker promoter can serve as a useful toolfor establishing which toxins or other small molecules can serve as RARligand mimics by, for example, exposing a recombinant cell of thisinvention to the compound and determining whether it induces activity ofan RAR biomarker promoter.

Conditions can be tested for their ability to induce or inhibit the RARresponse, as discussed above. RAR activating conditions to which cellscan be exposed for these tests include, for example, any compound orcondition that simulates RAR binding to its ligand binding domain.

2.11. Biological Response to TNFa and NFkB Activation

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to tumor necrosisfactor, alpha (TNFa) that is mediated by nuclear factorkappa-light-chain-enhancer of activated B cells (NFkB) (“NFkB biomarkerpromoter”). These NFkB biomarker promoters are identified in Table 1,section 11 and section 11a. The conditions used to induce the NFkBresponse was exposing cells to 20 ng/mL of TNFa for 8 hrs. Theexperimental conditions are set forth more completely in Example 11.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to TNFa. TNFa is a cytokine involved insystemic inflammation and is a member of a group of cytokines thatstimulate the acute phase reaction. NFkB is a heterodimerictranscription factor that translocates to the nucleus and mediates thetranscription of a vast array of proteins involved in cell survival andproliferation, inflammatory response, and anti-apoptotic factors and isactivated by TNFa. One can use such a promoter in an assay to determinewhether a test compound induces a NFkB-mediated response. This is done,for example, by exposing a cell containing an expression constructcomprising the transcription regulatory sequence operatively linked witha reporter sequence to a test compound. If the compound induces activityof the promoter, this means the compound induces a NFkB-mediatedresponse. Also, one can use the promoter in an assay to determinewhether a test compound inhibits a NFkB-mediated response. This is done,for example, by exposing a cell containing the expression construct to acondition that induces a NFkB-mediated response (for example, exposingthe cell to TNFa) and exposing the cell to the test compound. If thecompound inhibits the inducible activity of the promoter, this means thecompound inhibits the NFkB-mediated response.

The biological response to TNFa the “inflammation response induced byTNFa” involves a number of events at the cellular and molecular level.These events include NFkB-mediated expression of genes controllingsystemic inflammation. The activity of NFkB response biomarker promotersis, in turn, also correlated with these events.

In certain situations it is useful to activate an NFkB response.Activating NFkB activity is known to stimulate the immune system. TheNFkB response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to elicit an NFkB response.

Also, in certain situations it is desirable to inhibit a NFkB response.For example, inhibiting NFkB may inhibit the effects of chronicinflammation. The NFkB response biomarker promoters of this inventionare useful in discovering and evaluating pharmaceutical drugs and otherconditions for the ability to inhibit a NFkB response.

Conditions can be tested for their ability to induce or inhibit the NFkBresponse, as discussed above. NFkB activating conditions to which cellscan be exposed for these tests include, for example, any compound orcondition that simulates NFkB binding to genomic targets and affectingtranscription of those target genes.

2.12. Heat Shock Response

Several promoters have been identified, the activity of each of which ispositively correlated with the biological response to hyperthermia orheat shock signaling (“heat shock biomarker promoter”). These heat shockresponse biomarker promoters are identified in Table 1, section 12 andsection 12a. The conditions used to induce the heat shock response wasexposing cells to 43 degrees celsius for 8 hrs. The experimentalconditions are set forth more completely in Example 12.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to heat shock. When cells are exposed toelevated temperatures or other conditions that result in misfoldedproteins, they respond by increasing the expression of chaperoneproteins that help to stabilize proteins at higher temperatures. Thisresponse is mediated by the family of heat shock transcription factors.One can use such a promoter in an assay to determine whether a testcompound induces the heat shock response. This is done, for example, byexposing a cell containing an expression construct comprising thetranscription regulatory sequence operatively linked with a reportersequence to a test compound. If the compound induces activity of thepromoter, this means the compound induces a heat shock response. Also,one can use the promoter in an assay to determine whether a testcompound inhibits a heat shock response. This is done, for example, byexposing a cell containing the expression construct to a condition thatinduces a heat shock response (for example, exposing the cell to 43degrees C.) and exposing the cell to the test compound. If the compoundinhibits the inducible activity of the promoter, this means the compoundinhibits the heat shock response.

The biological response to heat shock (“heat shock response”) involves anumber of events at the cellular and molecular level. These eventsinclude heat shock transcription factor-mediated expression of genesencoding molecular chaperones. The activity of heat shock responsebiomarker promoters is, in turn, also correlated with these events.

In certain situations it is useful to activate the heat shock response.Activating chaperone proteins may serve as a protection in conditionsthat may otherwise denature proteins. The heat shock response biomarkerpromoters of this invention are useful in discovering and evaluatingpharmaceutical drugs and other conditions for the ability to elicit aheat shock response.

Also, in certain situations it is desirable to inhibit the heat shockresponse. For example, inhibiting heat shock may inhibit the effects ofchronic inflammation. The heat shock response biomarker promoters ofthis invention are useful in discovering and evaluating pharmaceuticaldrugs and other conditions for the ability to inhibit a heat shockresponse.

Conditions can be tested for their ability to induce or inhibit the heatshock response, as discussed above. Heat shock activating conditions towhich cells can be exposed for these tests include, for example, anycompound or condition that denatures or otherwise affects native proteinfolding.

2.13. Serum Response

Several promoters have been identified, the activity of each of which iscorrelated with the biological response to serum (“serum responsebiomarker promoter”). These serum response biomarker promoters areidentified in Table 1, section 13 and section 13a. The conditions usedto induce the serum response was exposing cells to 20% fetal bovineserum for 8 hrs. The experimental conditions are set forth morecompletely in Example 13.

More specifically, transcription regulatory sequences have been foundthat are induced when exposed to serum. When cells are exposed to serum,they activate the serum response transcription factor that directlyregulates a set of target genes. One can use such a promoter in an assayto determine whether a test compound induces the serum response. This isdone, for example, by exposing a cell containing an expression constructcomprising the transcription regulatory sequence operatively linked witha reporter sequence to a test compound. If the compound induces activityof the promoter, this means the compound induces a serum response. Also,one can use the promoter in an assay to determine whether a testcompound inhibits a serum response. This is done, for example, byexposing a cell containing the expression construct to a condition thatinduces a serum response (for example, exposing the cell to fetal bovineserum) and exposing the cell to the test compound. If the compoundinhibits the inducible activity of the promoter, this means the compoundinhibits the serum response.

The biological response to serum involves a number of events at thecellular and molecular level. These events include serum responsetranscription factor-mediated expression of genes involved in cell-cycleregulation, development, and muscle growth. The activity of serumresponse biomarker promoters is, in turn, also correlated with theseevents.

In certain situations it is useful to activate the serum response. Theserum response in some cases may stimulate muscle growth when needed.The serum response biomarker promoters of this invention are useful indiscovering and evaluating pharmaceutical drugs and other conditions forthe ability to elicit a serum response.

Also, in certain situations it is desirable to inhibit the serumresponse. For example, inhibiting serum may inhibit tumorigenesis orunregulated cell division. The serum response biomarker promoters ofthis invention are useful in discovering and evaluating pharmaceuticaldrugs and other conditions for the ability to inhibit a serum response.

Conditions can be tested for their ability to induce or inhibit theserum response, as discussed above. Serum response activating conditionsto which cells can be exposed for these tests include, for example, anycompound or condition that simulates the signaling molecules found inserum.

3. Expression Constructs

An expression construct is a recombinant nucleic acid moleculecomprising at least one expression control sequence operatively linkedwith another nucleotide sequence. A recombinant nucleic acid molecule isa nucleic acid molecule comprising two sequences that are not naturallyattached to one another, for example, sequences from different species.Two sequences are operably linked when they are placed in a functionalrelationship with each other so that activity of a first sequenceresults in an action on the other part. An expression control sequenceis operatively linked with a nucleotide sequence when expression of thenucleotide sequence is regulated by the action of the expression controlsequence. Expression control sequences include those that regulatetranscription of a nucleotide sequence, stability of the transcript ortranslation of the transcript.

This invention provides expression constructs comprising a biomarkertranscription regulatory sequence operatively linked with a reportersequence. The expression constructs of this invention can beincorporated into a vector or integrated, stably or transiently, into ahost cell chromosome.

3.1. Transcription Regulatory Sequences

Transcription regulatory sequences are nucleotide sequences that up- ordown-regulate transcription of another nucleotide sequence to which theyare operatively linked, e.g., a gene.

3.1.1. Promoters

Promoters are the best-characterized transcriptional regulatorysequences because of their predictable location immediately upstream oftranscription start sites. Promoters include sequences that modulate therecognition, binding and transcription initiation activity of the RNApolymerase. These sequences can be cis acting or can be responsive totrans acting factors. Promoters, depending upon the nature of theregulation, can be constitutive or regulated. They are often describedas having two separate segments: core and extended promoter regions.

The core promoter includes sequences that are sufficient for RNApolymerase recognition, binding and transcription initiation. The corepromoter includes the transcriptional start site, an RNA polymerasebinding site and other general transcription binding sites and is wherethe pre-initiation complex forms and the general transcription machineryassembles. It is generally within 50 nucleotides (nt) of thetranscription start site (TSS).

The extended promoter region includes the so-called proximal promoter,which extends to about 250 nucleotides upstream of the transcriptionalstart site (i.e., −250 nt). It includes primary regulatory elements suchas specific transcription factor binding sites. It has been found thatmany genes have transcription regulatory elements located furtherup-stream. In particular, a fragment that includes most of thetranscription regulatory elements of a gene can extend up to 700 nt ormore up-stream of the transcription start site. (See, e.g., U.S.2007-0161031.) In certain genes, transcription regulatory sequences havebeen found thousands of nucleotides upstream of the transcriptionalstart site.

3.1.2. Other Transcription Regulatory Sequences

Transcription regulatory sequences include nucleotide sequences thatconfer inducible expression of a gene (i.e., that require a substance orstimulus for increased transcription). When an inducer is present, orpresent at increased concentration, gene expression increases.Regulatory regions also include sequences that confer repression of geneexpression (i.e., a substance or stimulus decreases transcription). Whena repressor is present or at increased concentration, gene expressiondecreases. Regulatory regions typically bind one or more trans-acting orcis-acting proteins. Enhancers are known to influence gene expressionwhen positioned 5′ or 3′ of the gene, or when positioned in or a part ofan exon or an intron. Enhancers also can function at a significantdistance from the gene, for example, at a distance from about 3 Kb, 5Kb, 7 Kb, 10 Kb, 15 Kb or more.

Regulatory regions also include, in addition to transcription regulatorysequences, sequences in DNA or RNA molecules that regulate transcriptstability, transcript localization, facilitate translation, splicingsignals for introns, maintenance of the correct reading frame of thegene to permit in-frame translation of mRNA and, stop codons, leadersequences and fusion partner sequences, internal ribosome binding sites(IRES) elements for the creation of multigene, or polycistronic,messages, polyadenylation signals to provide proper polyadenylation ofthe transcript of a gene of interest and stop codons and can beoptionally included in an expression vector.

3.1.3. Biomarker Transcription Regulatory Sequences

This invention provides isolated nucleic acid sequences that function asbiomarker transcriptional regulatory sequences. As is well understood,DNA can be double stranded. The sequences of both strands, that is, onestrand and its complement, are considered sequences useful in thisinvention.

Expression constructs comprising the sequences of the SEQ ID NOs ofTable 1 operatively linked with a reporter sequence (e.g., a sequenceencoding luciferase) were found to have activity correlated with thebiological response indicated. Thus, transcription regulatory sequencesthat regulate transcription of genes identified in Table 1 are useful asbiomarker transcription regulatory sequences for those responses orpathways.

The sequences of Table 1 were selected from transcription regulatorysequences derived from an analysis of the human genome. The analysis isbased, in part, on work described in Cooper et al., Trinklein et al., US2007-0161031 and US 2009-0018031. In short, full-length cDNAs from theMammalian Gene Collection were aligned against the human genome.Sequences with less than 95% sequence identity, those with more than 200bases at the 5′ end of the cDNA that do not align with the genome, thosethat align to random sequence not assembled into reference chromosomesequences and those that represent alignment artifacts were filteredout. Alignment artifacts are identified as intronless (ungapped)alignments represented by a small number of independent cDNAs fromexisting cDNA libraries, as pseudogenes and as single exon genes. Morespecifically, a library of genetic sequences, such as GenBank, containsa number of molecules reported as cDNAs. When these sequences arealigned against the sequence of the genome, certain locations of thegenome are mapped by many reported cDNAs, so that the alignment cannotbe considered random: One can be highly confident that these locationsrepresent biologically relevant cDNAs and that the up-stream sequencesare active transcription regulatory sequences. Other locations in thegenome are mapped by few reported cDNAs or none. If the cDNA sequencesare unspliced (that is they contain no introns) and the number of cDNAsmapping to a location in the genome is no more than what one wouldexpect under a random model, then these alignments are consideredartifacts. Sequences upstream of the 5′ end of these cDNAs (thetranscription start site) were selected as transcription regulatorysequence.

Individual genes can have more than one transcriptional start site, andin turn multiple promoters containing different transcriptionalregulatory sequences. Therefore in many cases we experimentally testedmultiple promoters for each gene to identify the precise promoter thatregulates the biological response of interest.

Each sequence identified in Table 1 by SEQ ID NO is useful as biomarkerregulatory sequence of this invention. For example, the transcriptionregulatory sequence can be the entire sequence of the given SEQ ID NO.Alternatively, transcription regulatory sequence can be comprised withina longer sequence from the genome from which the sequence of the SEQ IDNO is taken. For example, this sequence can be upstream of the 5′ endindicated in the SEQ ID NO. The sequences of Table 1 are humansequences. In other embodiments, the transcription regulatory sequencecan comprise a fragment of a sequence of Table 1. Such fragments cancomprise at least 25 nt, at least 50 nt, at least 100 nt, at least 250nt, at least 500 nt, at least 600 nt, at least 700 nt or at least 900 ntof the sequence of the provided SEQ ID NO.

Any transcription regulatory sequence of a biomarker gene of Table 1 canbe used in the expression constructs of this invention. This includes,for example, the transcription start site, the core promoter, theextended promoter, an enhancer region, an inducer region, a repressorregion, insulators, suppressors or transcription factor binding site.For example, the transcription regulatory sequence can comprise asequence sufficient to initiate transcription of a second sequence towhich it is operatively linked.

In certain embodiments, the sequence includes a sequence extending atleast 250 nucleotides up-stream of the transcription start site.However, closer fidelity of activity to the natural environment can beachieved by including transcription regulatory sequences that arefurther up-stream of the transcription start site, e.g., those thatexist in the extended promoter region. For example, the sequence canextend at least or no more than any of −300 nt, −400 nt, −500 nt, −600nt, −700 nt, −800 nt, −900 nt, −1000 nt, −1200 nt, −1500 nt, −1800 nt,−2000 nt or −3000 nt from a transcription start site. Also, the sequencecan comprise sequence downstream of the transcription start site. Forexample, up to +10 nt, +20 nt, up to +50 nt, up to +100 nt or more than+100 nt. All combinations of these ranges are contemplated. So, forexample, the transcription regulatory sequence can include, consistessentially of, or consist of a sequence that spans a range from about+100 to about −3000, about +50 to about −2000, about +20 to about −1800,about +20 to about −1500, about +10 to about −1500, about +10 to about−1200, about +20 to about −1000, about +20 to about −900, about +20 toabout −800, about +20 to about −700, about +20 to about −600, about +20to about −500, about +20 to about −400, or about +20 to about −300,relative to a transcription start site.

The transcription regulatory sequence can be any polymorphic form of asequence of Table 1. A polymorphic form is one of two or moregenetically determined alternative sequences or alleles in a population.The site of the alternative form is referred to as the locus.Polymorphic forms can occur at any frequency in a population. Allelesare those polymorphic forms that occur with a frequency of preferablygreater than 1%, greater than 10% or greater than 20% of a population. Apolymorphism may comprise one or more base changes, an insertion, arepeat, or a deletion. A polymorphic locus may be as small as one basepair. Polymorphic forms can include single nucleotide polymorphisms(SNPs), insertions, deletions and repeated sequences. For example,polymorphisms include variable number of tandem repeats (VNTR's),hypervariable regions, minisatellites, dinucleotide repeats,trinucleotide repeats, tetranucleotide repeats, simple sequence repeats,and insertion elements such as Alu. The allelic form occurring mostfrequently in a selected population is sometimes referred to as thewildtype form. It is estimated that there are as many as 3×10⁶ SNPs inthe human genome. Diploid organisms may be homozygous or heterozygousfor allelic forms. A diallelic polymorphism has two forms. A triallelicpolymorphism has three forms. A polymorphism between two nucleic acidscan occur naturally, or be caused by exposure to or contact withchemicals, enzymes, or other agents, or exposure to agents that causedamage to nucleic acids, for example, ultraviolet radiation, mutagens orcarcinogens.

Polymorphic forms typically will share at least 95% sequence identity,at least 96% sequence identity, at least 97% sequence identity, at least98% sequence identity, at least 99% sequence identity, at least 99.5%sequence identity, at least 99.75% sequence identity, at least 99.9%sequence identity over a comparison window of at least 200 nucleotideswith a sequence of any the SEQ ID NOs given here. Alternatively, thesequence can hybridize under stringent conditions with a sequence of anySEQ ID NO given here. Such a sequence can be at least 200 nt, at least500 nt, at least 600 nt, at least 700 nt, at least 800 nt, etc.

3.1.4 Sequence Identity and Hybridization

Terms used to describe sequence relationships between two or morenucleotide sequences or amino acid sequences include “referencesequence,” “selected from,” “comparison window,” “identical,”“percentage of sequence identity,” “substantially identical,”“complementary,” and “substantially complementary.”

A “reference sequence” is a defined sequence used as a basis for asequence comparison and may be a subset of a larger sequence, e.g., acomplete cDNA, protein, or gene sequence.

Because two polynucleotides or polypeptides each may comprise (1) asequence (i.e., only a portion of the complete polynucleotide orpolypeptide sequence) that is similar between the two polynucleotides,or (2) a sequence that is divergent between the two polynucleotides,sequence comparisons between two (or more) polynucleotides orpolypeptides are typically performed by comparing sequences of the twopolynucleotides over a “comparison window” to identify and compare localregions of sequence similarity.

A “comparison window” refers to a conceptual segment of typically atleast 12 consecutive nucleotides or 4 consecutive amino acid residuesthat is compared to a reference sequence. The comparison windowfrequently has a length of at least 15 or at least 25 nucleotides or atleast 5 or at least 8 amino acids. The comparison window may compriseadditions or deletions (i.e., gaps) of about 20 percent or less ascompared to the reference sequence (which does not comprise additions ordeletions) for optimal alignment of the two sequences. Optimal alignmentof sequences for aligning a comparison window may be conducted bycomputerized implementations of algorithms (GAP, BESTFIT, FASTA, andTFASTA in the Wisconsin Genetics Software Package Release 7.0, GeneticsComputer Group, 575 Science Dr., Madison, Wis.) or by inspection, andthe best alignment (i.e., resulting in the highest percentage ofhomology over the comparison window) generated by any of the variousmethods is selected.

A subject nucleotide sequence or amino acid sequence is “identical” to areference sequence if the two sequences are the same when aligned formaximum correspondence over the length of the nucleotide or amino acidsequence.

The “percentage of sequence identity” between two sequences iscalculated by comparing two optimally aligned sequences over acomparison window, determining the number of positions at which theidentical nucleotide or amino acid occurs in both sequences to yield thenumber of matched positions, dividing the number of matched positions bythe total number of positions in the window of comparison (i.e., thewindow size), and multiplying the result by 100 to yield the percentageof sequence identity.

Unless otherwise specified, the comparison window used to compare twosequences is the length of the shorter sequence.

Methods are described further in Natl. Acad. Sci. USA 85:2444; Higgins &Sharp (1988) Gene 73:237-244; Higgins & Sharp, CABIOS 5:151-153 (1989);Corpet et al. (1988) Nucleic Acids Research 16:10881-90; Huang et al.(1992) Computer Applications in the Biosciences 8:155-65; and Pearson etal. (1994) Methods in Molecular Biology 24:307-31. Alignment is alsooften performed by inspection and manual alignment.

A subject nucleotide sequence or amino acid sequence is “substantiallyidentical” to a reference sequence if the subject amino acid sequence ornucleotide sequence has at least 80% sequence identity over a comparisonwindow. Thus, sequences that have at least 85% sequence identity, atleast 90% sequence identity, at least 95% sequence identity, at least98% sequence identity or at least 99% sequence identity with thereference sequence are also “substantially identical. Two sequences thatare identical to each other are, of course, also “substantiallyidentical”.

“Hybridizing specifically to” or “specific hybridization” or“selectively hybridize to”, refers to the binding, duplexing, orhybridizing of a nucleic acid molecule preferentially to a particularnucleotide sequence under stringent conditions when that sequence ispresent in a complex mixture (e.g., total cellular) DNA or RNA.

The term “stringent conditions” refers to conditions under which a probewill hybridize preferentially to its target subsequence, and to a lesserextent to, or not at all to, other sequences. “Stringent hybridization”and “stringent hybridization wash conditions” in the context of nucleicacid hybridization experiments such as Southern and northernhybridizations are sequence dependent, and are different under differentenvironmental parameters. An extensive guide to the hybridization ofnucleic acids is found in Tijssen (1993) Laboratory Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic AcidProbes part I chapter 2 “Overview of principles of hybridization and thestrategy of nucleic acid probe assays”, Elsevier, New York.

Generally, highly stringent hybridization and wash conditions areselected to be about 5° C. lower than the thermal melting point (Tm) forthe specific sequence at a defined ionic strength and pH. The Tm is thetemperature (under defined ionic strength and pH) at which 50% of thetarget sequence hybridizes to a perfectly matched probe. Very stringentconditions are selected to be equal to the Tm for a particular probe.

An example of stringent hybridization conditions for hybridization ofcomplementary nucleic acids which have more than 100 complementaryresidues on a filter in a Southern or northern blot is 50% formalin with1 mg of heparin at 42° C., with the hybridization being carried outovernight. An example of highly stringent wash conditions is 0.15 M NaClat 72° C. for about 15 minutes. An example of stringent wash conditionsis a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook et al. for adescription of SSC buffer). Often, a high stringency wash is preceded bya low stringency wash to remove background probe signal. An examplemedium stringency wash for a duplex of, e.g., more than 100 nucleotides,is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for aduplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15minutes. In general, a signal to noise ratio of 2× (or higher) than thatobserved for an unrelated probe in the particular hybridization assayindicates detection of a specific hybridization.

3.1.5 Collections

In certain embodiments, this invention provides collections thatcomprise the biomarker transcription regulatory sequences of thisinvention. The collections include isolated nucleic acids, that is,nucleic acids isolated away from their natural environment or existingin a composition in which the nucleic acid is the predominant species oforganic or non-solvent molecule. The collections also include expressionconstructs of this invention and cells comprising the expressionconstructs of this invention.

In certain embodiments, the transcription regulatory sequences of thecollection consist of or consist essentially of the biomarkertranscription regulatory sequences of this invention. In otherembodiments, at least 20%, at least 30%, at least 40%, at least 50%, atleast 60%, at least 70%, at least 90%, at least 95%, at least 97% or atleast 99% of the transcription regulatory sequences of the collectionare transcription regulatory sequences of this invention. So, forexample, at least 20% of the transcription regulatory sequences of thecollection can be biomarkers selected from a selected from a section ofTable 1, which are biomarkers for the same biological response.Alternatively, the at least 20% can be selected from biomarkertranscription regulatory sequences of at least 2, at least 3, at least4, at least 5, at least 6, at least 7, at least 8, at least 9, at least10, at least 11, at least 12 or at least 13 different biologicalresponses, e.g., different sections of Table 1, in which case,biomarkers for a plurality of different biological responses will berepresented. The collections can comprise no more than 2, no more than5, no more than 10, no more than 50, no more than 100, no more than 500,no more than 1000 or no more than 5000 transcription regulatorysequences.

3.2. Reporters

In certain embodiments, a transcription regulatory sequence isoperatively linked with a heterologous reporter sequence. A reportersequence is heterologous if it is not naturally under transcriptionalregulatory control of the transcription regulatory sequence. For examplethe transcription regulatory sequence and the reporter can be fromdifferent species or the reporter can be an artificially constructedsequence.

A reporter sequence can be any sequence that allows for the detection ofa molecule of interest, such as a protein expressed by a cell, or abiological particle. Typical reporter sequences include, include, forexample, those encoding light emitting proteins (e.g., luciferase (see,e.g., U.S. Pat. No. 5,292,658), fluorescent proteins (e.g., red, blueand green fluorescent proteins (see, e.g., U.S. Pat. No. 6,232,107,which provides GFPs from Renilla species and other species and U.S. Pat.No. 5,625,048), lacZ (e.g., from E. coli), alkaline phosphatase,secreted embryonic alkaline phosphatase (SEAP), chloramphenicol acetyltransferase (CAT), hormones and cytokines and other such well-knownproteins. For expression in cells, a nucleic acid encoding the reportersequence can be expressed as a fusion protein with a protein of interestor under to the control of a promoter of interest. The expression ofthese reporter genes can also be monitored by measuring levels of mRNAtranscribed from these genes or from detection of the translatedpolypeptide.

In collections using proteins that emit a detectable signal it may beuseful, but not essential, for all of the reporter proteins to emit thesame signal. This simplifies detection during high-throughput methods.

Alternatively, the expression constructs in the collection can containdifferent reporter sequences that emit different detectable signals. Forexample, each reporter sequence can be a light emitting reporter thatemits light of a different, distinguishable color. Alternatively, thereporter sequence in each of the constructs can be a unique,pre-determined nucleotide barcode. This allows assaying a large numberof the nucleic acid segments in the same batch or receptacle of cells.In an embodiment, in each construct a unique promoter sequence is clonedupstream of a unique barcode reporter sequence yielding a uniquepromoter/barcode reporter combination. The active promoter can drive theproduction of a transcript containing the unique barcode sequence. Thus,in a collection of expression constructs, each promoter's activityproduces a unique transcript whose level can be measured. Since eachreporter is unique, the library of expression constructs can betransfected into one large pool of cells (as opposed to separate wells)and all of the RNAs may be harvested as a pool. The levels of each ofthe barcoded transcripts can be detected using a microarray with thecomplementary barcode sequences. So the amount of fluorescence on eacharray spot corresponds to the strength of the promoter that drove thenucleotide barcode's transcription.

In certain embodiments of this invention, a cell or collection of cellscan comprise a plurality of expression constructs of this inventionwhich include biomarker expression control sequences of a plurality ofdifferent biological responses. In this case, it may be useful to usereporters for each expression control sequence that can be distinguishedfrom each other, e.g., by emitting a different color or having adifferent bar code.

Optionally, an expression construct can contain both a first reportersequence and a second reporter sequence. The first reporter sequence anda second reporter sequence are preferred to be different. For example,the first reporter sequence may encode the same reporter protein (e.g.,luciferase or GFP), and the second reporter sequence may be a uniquenucleotide barcode. In this way, transcription can yield a hybridtranscript of a reporter protein coding region and a unique barcodesequence. Such a construct could be used either in areceptacle-by-receptacle approach for reading out the signal emitted bythe reporter protein (e.g., luminescence) and/or in a pooled approach byreading out the barcodes.

By using the unique, molecular barcode for each member of thecollection, a large collection can be assayed in a single receptacle(such as a vial or a well in a plate) rather than in thousands ofindividual receptacles. This approach is more efficient and economic asit can reduce costs at all levels: reagents, plasticware, and labor.

3.3 Vectors and Chromosomes

The recombinant nucleic acid molecule can be further comprised within avector that can be used to either infect or transiently or stablytransfect cells and that may be capable of replicating inside a cell.Expression constructs can be made part of vectors, such as plasmids,cosmids, viral genomes, bacterial artificial chromosomes and the like.They also can be integrated stably into a chromosome of a host cell.

Any suitable vector can be used. There are many known in the art.Examples of vectors that can be used include, for example, plasmids ormodified viruses. The vector is typically compatible with a given hostcell into which the vector is introduced to facilitate replication ofthe vector and expression of the encoded reporter. Examples of specificvectors that may be useful in the practice of the present inventioninclude, but are not limited to, E. coli bacteriophages, for example,lambda derivatives, or plasmids, for example, pBR322 derivatives or pUCplasmid derivatives; phage DNAs, e.g., the numerous derivatives of phage1, e.g., NM989, and other phage DNA, e.g., M13 and filamentous singlestranded phage DNA; yeast vectors such as the 2 mu plasmid orderivatives thereof; vectors useful in eukaryotic cells, for example,vectors useful in insect cells, such as baculovirus vectors, vectorsuseful in mammalian cells such as retroviral vectors, adenoviralvectors, adenovirus viral vectors, adeno-associated viral vectors, SV40viral vectors, herpes simplex viral vectors and vaccinia viral vectors;vectors derived from combinations of plasmids and phage DNAs, plasmidsthat have been modified to employ phage DNA or other expression controlsequences; and the like.

4. Cells Containing Expression Constructs

In another aspect this invention provides recombinant cells comprisingthe expression constructs of this invention. Two different embodimentsare contemplated in particular.

In a first embodiment each cell or group of cells comprises a differentmember of the expression library. Such a library of cells isparticularly useful with the arrays of this invention. Typically, thelibrary is indexed. For example, each different cell harboring adifferent expression vector can be maintained in a separate containerthat indicates the identity of the genomic segment within. The indexalso can indicate the particular gene or genes that is/are under thetranscriptional regulatory control of the sequences naturally in thegenome.

In a second embodiment, a culture of cells is transfected with a libraryof expression constructs so that all of the members of the library existin at least one cell and each cell has at least one member of theexpression library. In this embodiment, a cell can comprise more thanone different expression constructs (e.g., having transcriptionregulatory sequences of different genes). The second embodiment isparticularly useful with libraries in which the reporter sequences areunique sequences that can be detected independently.

As used herein the term cells and grammatical equivalents herein inmeant any cell, preferably any prokaryotic or eukaryotic cell.

Suitable prokaryotic cells include, but are not limited to, bacteriasuch as E. coli, various Bacillus species, and the extremophile bacteriasuch as thermopiles, etc.

Suitable eukaryotic cells include, but are not limited to, fungi such asyeast and filamentous fingi, including species of Aspergillus,Trichoderma, and Neurospora; plant cells including those of corn,sorghum, tobacco, canola, soybean, cotton, tomato, potato, alfalfa,sunflower, etc.; and animal cells, including fish, birds and mammals.Suitable fish cells include, but are not limited to, those from speciesof salmon, trout, tulapia, tuna, carp, flounder, halibut, swordfish, codand zebrafish. Suitable bird cells include, but are not limited to,those of chickens, ducks, quail, pheasants and turkeys, and other junglefoul or game birds. Suitable mammalian cells include, but are notlimited to, cells from horses, cows, buffalo, deer, sheep, rabbits,rodents such as mice, rats, hamsters and guinea pigs, goats, pigs,primates, marine mammals including dolphins and whales, as well as celllines, such as human cell lines of any tissue or stem cell type, andstem cells, including pluripotent and non-pluripotent, and non-humanzygotes.

Useful cell types include primary and transformed mammalian cell lines.Suitable cells also include those cell types implicated in a widevariety of disease conditions, even while in a non-diseased state.Accordingly, suitable cell types include, but are not limited to, tumorcells of all types (e.g. melanoma, myeloid leukemia, carcinomas of thelung, breast, ovaries, colon, kidney, prostate, pancreas and testes),cardiomyocytes, dendritic cells, endothelial cells, epithelial cells,lymphocytes (T-cell and B cell), mast cells, eosinophils, vascularintimal cells, macrophages, natural killer cells, erythrocytes,hepatocytes, leukocytes including mononuclear leukocytes, stem cellssuch as haemopoetic, neural, skin, lung, kidney, liver and myocyte stemcells (for use in screening for differentiation and de-differentiationfactors), osteoclasts, chondrocytes and other connective tissue cells,keratinocytes, melanocytes, liver cells, kidney cells, and adipocytes.In some embodiments, the cells used with the methods described hereinare primary disease state cells, such as primary tumor cells. Suitablecells also include known research cell lines, including, but not limitedto, Jurkat T cells, NIH3T3 cells, CHO, COS, HT1080 human fibrosarcomacells, HepG2 hepatocarcinoma cells, HeLa cells, etc. See the ATCC cellline catalog, hereby expressly incorporated by reference.

In some embodiments the cells used in the present invention are takenfrom an individual. In some embodiments the individual is a mammal, andin other embodiments the individual is human.

Exogenous DNA may be introduced to cells by lipofection,electroporation, or infection. Libraries in such cells may be maintainedin growing cultures in appropriate growth media or as frozen culturessupplemented with Dimethyl Sulfoxide and stored in liquid nitrogen.

4.1. Transient Expression

In certain embodiments this invention provides transiently transformedcells. In this embodiment, vector DNA is delivered to living cells usinga transfection reagent such as a lipofection compound. The cells expressthe content of this vector construct but the cell does not incorporatethe vector sequence in its genome. A typical transient transfectionexperiment involves seeding cells in a plate or dish, then 24 hourslater transfecting the vector DNA, then 12-24 hrs later applying astimulus of interest, and then recording the reporter signal.

4.2. Stably Transformed Cells

In other embodiments, this invention provides stably transformed cells.In this embodiment, the vector DNA contains a gene for a mammalianselectable marker such as hygromycin. The vector is delivered to livingcells using a transfection reagent such as a lipofection compound or inthe form of a virus, and the cells are grown in the presence of theselecting antibiotic. Over the course of 5-20 or more cell passages,only cells that have integrated the vector DNA into their genome areselected for.

5. Devices and Kits

This invention provides kits and devices. The kits can include allreagents necessary to transiently transfect, infect, or transduce cellsand perform assays. For example, the kits can include one or morecontainers comprising one or more expression constructs of thisinvention. They also can contain a container comprising a substrate fora reporter molecule made by the expression construct. The kit also cancontain containers comprising appropriate solutions for carrying out theassay, such as appropriate buffers. The kit also can containinstructions on how to carry out the assay. The kit can also contain acontainer comprising cells to be transfected by the expressionconstruct. In certain embodiments, the cells will be stably transformedto contain the expression construct. In certain embodiments, the kitcontains microtiter plates, such as those having wells in multiples of96, which are typically used in research.

6. Methods

6.1 Test Conditions

Certain methods of this invention involve exposing cells to testconditions. A test condition can be any condition different than acontrol condition to which a cell is exposed. Test conditions include,for example, contacting the cell with a test composition, exposing thecell to a test environmental condition, over-expressing or knocking downexpression of a particular gene of interest in the cell, or combinationsof these.

Test compositions include individual compounds and mixtures ofcompounds, e.g., a library of compounds. A compound can be any elementor molecule, for example, small organic molecules and biopolymers. Drugcandidates useful as test compositions in this invention include smallorganic molecules and biological molecules, e.g., biologics. Organicmolecules used as pharmaceuticals generally are small organic moleculestypically having a size up to about 5000 Da, up to about 2000 Da, or upto about 1000 Da. Certain hormones are small organic molecules. Organicbiopolymers also are used as test compositions. These include, forexample, polypeptides (e.g., peptides and proteins), polynucleotides(e.g., oligonucleotides or nucleic acids (e.g., inhibitorypolynucleotides, such as ribozymes, antisense molecules or interferingRNA molecules), carbohydrates, lipids and molecules that combine these,for example glycoproteins, glycolipids and lipoproteins. Certainhormones are biopolymers. Antibodies find increasing use as biologicalpharmaceuticals. U.S. publication 2009-0035216 provides a list ofantibody drugs. This list includes, for example herceptin, bevacizumab,avastin, erbitux and synagis (cell adhesion molecules).

6.2 Assays

This invention provides assays for determining whether and to whatextent a test condition modulates a biological response. In certainembodiments, the methods involve exposing a recombinant cell of thisinvention to a test condition and measuring the amount of activity of abiological response biomarker promoter of this invention. In certainembodiments, the cells tested do not exhibit the biological response,and the methods involve exposing the cells to a test condition anddetermining whether the response is invoked. In other embodiments, thecells are exhibiting the biological response, e.g., by exposing thecells to conditions that elicit the response and then exposing the cellsto the test condition. The expression of the reporter indicates theactivity of the biomarker expression control sequence. The activity ofthe biomarker, in turn, indicates the activity of the biologicalresponse for which it is a biomarker.

Measuring a response includes quantitative and qualitativedeterminations. Qualitative measurement includes measuring a response orlack of response, regardless of intensity. A quantitative responsegenerally involves measuring the intensity of a response.

The assays rely in part on the correlation between the activity ofbiomarker promoters and the activity of biological responses. Thiscorrelation can be positive (e.g., stimulation of biomarker activitycorrelates with activation of the response, or inhibition of thebiomarker correlates with inhibition of the response) or the correlationcan be negative (e.g., stimulating activity of the biomarker correlateswith inhibition of the response, or inhibition of biomarker activitycorrelates with activation of the biological response). Thus, biomarkeractivity (its induction or inhibition of induction) functions as a proxyfor the activity of the biological response. This, in turn, allows oneto determine whether a test condition modulates (e.g., activates orinhibits) a biological response, based on the ability of the testcondition to modulate activity of the biomarker promoter and thecorrelation of activity of the biomarker promoter with the activity ofthe biological response. A test condition that modulates or altersactivity of a biomarker transcription regulatory sequence, by extension,modulates or alters activity of the biological response for which thetranscription regulatory sequence is a biomarker.

This invention contemplates a number of different types of assays. Inone assay, a cell comprising an expression construct of this inventionis exposed to a test condition and the activity of the biomarkerexpression control sequence is determined based on expression of thereporter sequence. In another assay, a biomarker expression controlsequence for a single biological response is exposed to a plurality ofdifferent test conditions, e.g., a plurality of different testcompositions, and the effect of each test condition on the activity ofthe biomarker is determined. This can be, for example, a high throughputassay in which tens, hundreds or thousands of conditions are tested. Inanother embodiment, a single test condition is tested for the ability tomodulate activity of one or more biomarkers for a plurality of differentbiological responses. For example, one can test biomarkers for at least2, at least 5, at least 10 or at least 13 different biologicalresponses.

A container (e.g., a multiwell plate array) containing cells harboringan expression construct of this invention is useful for high-throughputscreening of promoter activity. A cell comprising an expressionconstruct that comprises a biological response biomarker promoteroperably linked with a reporter gene is exposed to a test conditionunder conditions chosen by the operator. Cells in which the promotersare “turned on” will express the reporter sequences under theirtranscriptional control. The investigator then checks each well of thedevice to measure the amount of reporter transcribed. Generally, thisinvolves measuring the signal produced by a reporter protein encoded bythe reporter sequence. For example, if the reporter protein is a lightemitting reporter, then the amount of light produced in each cell ismeasured. In the case of a fluorescent protein, light can be directed toeach well to induce fluorescence. The amount of signal measured is afunction of the expression of the reporter sequence which, in turn, is afunction of the activity of the transcriptional regulatory sequences. Incertain methods, the assay is multiplexed. A number of compounds, e.g.,a library of compounds can be tested. This can involve testing eachcompound against a recombinant cell of this invention.

The choice of a proper detection system for a particular application iswell within the abilities of one of skill in the art. Exemplarydetection means include, but are not limited to, detection by unaidedeye, light microscopy using the eye or an optical sensor as thedetector, confocal microscopy, laser scanning confocal microscopy,imaging using quantum dot color, fluorescence spectrum or other quantumdot property and wide-field imaging with a 2D CCD camera. In anexemplary embodiment, the device is a fluorescent plate reader. Forexample, the assay can be performed in a multiwell plate, e.g., a platewith multiples of 96 wells (e.g., 96-well plate, 384-well plate,1536-well plate). In assays in which the reporter is luminescent orfluorescent molecule, the reporter may have to be induced to producelight. For example, in assays involving luciferase, a substrate for theenzyme is provided. In the case of fluorescent proteins, light of anexciting wavelength is provided. Commercially available microplateluminometers can be used to detect the signal. These are available from,for example, Tecan, Molecular Devices and Berthold.

Assays can involve creation of a standard curve against whichmeasurements are compared to quantify the amount of expression.

It also can be useful to identify differences in transcriptionregulatory sequence activity in two cell types. For example geneexpression differs when cells transform from normal to cancerous.Promoters that are overactive in cancer cells may be targets ofpharmacological intervention. The arrays of this invention are useful toidentify such transcription regulatory sequences. Accordingly, theinvestigator provides two sets of arrays comprising expressionconstructs in the wells. Once cell type is used for transformation in afirst device and a second cell type, for transformation in a seconddevice. The expression of reporter sequences between the two devices iscompared to identify those expressed differently in the two cell types.

Using expression constructs in which the transcription regulatorysequences are operably linked to unique reporter sequences opens thepossibility of performing tests without the use of multiwell plates. Insuch situations a single culture of cells contains the entire expressionlibrary distributed among the cells. The culture can be incubated underconditions chosen by the investigator. Then the expression products areisolated. Reporters that emit different colors can be used. Asdescribed, if the reporter is a barcode, because each expression vectorhas a unique nucleotide sequence tag or barcode associated with itspartner nucleic acid segment, the amount of each of the reportersequences can be measured by measuring the amount of transcriptcomprising each unique sequence. For example, the molecules can bedetected on a DNA array that contains probes complementary to the uniquesequences. The amount of hybridization to each probe indicates theamount of the reporter sequence expressed, which, in turn, reflects theactivity of the transcription regulatory sequences.

EXAMPLES 1. Biological Responses

1.1 Biological Response to Hypoxia

Transient transfection assays were conducted in HT1080 humanfibrosarcoma cells (ATCC, Manassas, Va.) in 96-well white plates. After5,000 cells per well were seeded in culture medium for 24 hr, 50 ng ofplasmid DNA per well was transfected with Fugene-6 transfection reagent(Roche Diagnostics, Indianapolis, Ind.) according to Fugene standardprotocols. After 16 hrs, the transfection medium was removed and freshculture medium was added into each well, and 3 replicates of eachconstruct were moved into a chamber containing 1% oxygen, 5% CO₂, and94% nitrogen. Cells were kept in the low oxygen condition for 24 hrs. Inaddition, 3 replicates of each construct were treated with 100 uM DFOfor 24 hrs. Furthermore, 3 replicates of each construct remained innormal oxygen conditions and were not treated with DFO to serve asuntreated control replicates. After induction, 100 uL of Steady-Glo(Promega) was added into each well, incubated at room temperature for 30min, and then read in a standard plate luminometer (Molecular Devices,Sunnyvale, Calif.). Each treatment was assayed in triplicate, and theaverage of the 3 replicates without hypoxia induction and the average ofthe 3 replicates with hypoxia induction were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the hypoxia response in this assay, and that can be usedas biomarkers for the hypoxia response, are identified in Table 1,section 1 and section 1a.

1.2. Biological Response to Estrogen (β-Estradiol)

Transient transfection assays were conducted in HT1080 humanfibrosarcoma cells (ATCC, Manassas, Va.) in 96-well white plates. First,10,000 cells per well were seeded in charcoal stripped culture mediumfor 24 hr. Next, 50 ng of reporter plasmid DNA and 10 ng of an ER cDNAexpression plasmid (Origene) per well were transfected with Fugene-6transfection reagent (Roche Diagnostics, Indianapolis, Ind.) accordingto Fugene standard protocols. After 16 hrs, the transfection medium wasremoved and fresh culture medium with or without the addition of aninducing compound was added to each well. For the no treatment control,only fresh media was added to the wells. β-estradiol (Sigma) was addedto the media of the treated samples at a final concentration of 10 nM.Cells were incubated for 24 hrs after induction. After 24 hrs, 100 uL ofSteady-Glo (Promega) was added into each well, incubated at roomtemperature for 30 min, and then read in a standard plate luminometer(Molecular Devices, Sunnyvale, Calif.). Each treatment for each reporterconstruct was assayed in triplicate, and the average of the 3 replicateswithout treatment and the average of the 3 replicates with treatmentwere recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the estrogen response in this assay, and that can beused as biomarkers for the estrogen response, are identified in Table 1,section 2 and section 2a.

1.3. Biological Response to Artificial Androgen (Methyltrienolone)

Transient transfection assays were conducted in HT1080 humanfibrosarcoma cells (ATCC, Manassas, Va.) in 96-well white plates. First,10,000 cells per well were seeded in charcoal stripped culture mediumfor 24 hr. Next, 50 ng of reporter plasmid DNA and 10 ng of an AR cDNAexpression plasmid (Origene) per well were transfected with Fugene-6transfection reagent (Roche Diagnostics, Indianapolis, Ind.) accordingto Fugene standard protocols. After 16 hrs, the transfection medium wasremoved and fresh culture medium with or without the addition of aninducing compound was added to each well. For the no treatment control,only fresh media was added to the wells. Methyltrienolone (R1881) wasadded to the media of the treated samples at a final concentration of 10nM. Cells were incubated for 24 hrs after induction. After 24 hrs, 100uL of Steady-Glo (Promega) was added into each well, incubated at roomtemperature for 30 min, and then read in a standard plate luminometer(Molecular Devices, Sunnyvale, Calif.). Each treatment for each reporterconstruct was assayed in triplicate, and the average of the 3 replicateswithout treatment and the average of the 3 replicates with treatmentwere recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the androgen response in this assay, and that can beused as biomarkers for the androgen response, are identified in Table 1,section 3 and section 3a.

1.4 Biological Response Mediated by p53

Transient transfection assays were conducted in HT1080 humanfibrosarcoma cells (ATCC, Manassas, Va.) in 96-well white plates. First,5,000 cells per well were seeded in standard culture medium for 24 hr.Next, 50 ng of reporter plasmid DNA per well was transfected withFugene-6 transfection reagent (Roche Diagnostics, Indianapolis, Ind.)according to Fugene standard protocols. After 16 hrs, the transfectionmedium was removed and fresh culture medium with or without the additionof an inducing compound was added to each well. For the no treatmentcontrol, only fresh media was added to the wells. The p53 protein wasinduced by two separate treatments: nutlin (Sigma) was added to themedia at a final concentration of 10 uM, and doxorubicin (Calbiochem)was added to the media at a final concentration of 200 ng/ml. Cells wereincubated for 24 hrs after induction. After 24 hrs, 100 uL of Steady-Glo(Promega) was added into each well, incubated at room temperature for 30min, and then read in a standard plate luminometer (Molecular Devices,Sunnyvale, Calif.). Each treatment for each reporter construct wasassayed in triplicate, and the average of the 3 replicates withouttreatment and the average of the 3 replicates with treatments wererecorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the p53 activation response in this assay, and that canbe used as biomarkers for the p53 activation response, are identified inTable 1, section 4 and section 4a.

1.5 Biological Response to Inhibitors or Activators of CholesterolBiosynthesis

Transient transfection assays were conducted in HepG2 hepatocarcinomacells (ATCC, Manassas, Va.) in 96-well white plates. First, 10,000 cellsper well were seeded in delipidated culture medium for 24 hr. Next, 100ng of reporter plasmid DNA per well was transfected with Fugene-6transfection reagent (Roche Diagnostics, Indianapolis, Ind.) accordingto Fugene standard protocols. After 16 hrs, the transfection medium wasremoved and fresh culture medium with or without the addition of aninducing compound was added to each well. For the no treatment control,only fresh media was added to the wells. Inductions were done by threeseparate treatments: lovastatin (Sigma) (HMG-CoA reductase inhibitor)was added to the media at a final concentration of 1 uM, synthechol(Sigma) (activator of cholesterol utilization pathway) was added to themedia at a final concentration of 5 ug/ml, and U1866A (Sigma) (inhibitorof intracellular cholesterol transport) was added to the media at afinal concentration of 1 uM. Cells were incubated for 24 hrs afterinduction. After 24 hrs, 100 uL of Steady-Glo (Promega) was added intoeach well, incubated at room temperature for 30 min, and then read in astandard plate luminometer (Molecular Devices, Sunnyvale, Calif.). Eachtreatment for each reporter construct was assayed in triplicate, and theaverage of the 3 replicates without treatment and the average of the 3replicates with treatments were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the cholesterol response in this assay, and that can beused as biomarkers for the cholesterol response, are identified in Table1, section 5 and section 5a.

1.6 Biological Response to Interferons

Transient transfection assays were conducted in Hela cells (ATCC,Manassas, Va.) in 96-well white plates. First, 10,000 cells per wellwere seeded in a starvation medium (phenol-free Opti-MEM) for 24 hr.Next, 100 ng of reporter plasmid DNA per well was transfected withFugene-6 transfection reagent (Roche Diagnostics, Indianapolis, Ind.)according to Fugene standard protocols. After 16 hrs, the transfectionmedium was removed and fresh culture medium with or without the additionof an inducing compound was added to each well. For the no treatmentcontrol, only fresh media was added to the wells. Inductions were doneby two separate treatments: interferon alpha (Calbiochem) was added tothe media at a final concentration of 500 U/ml, and interferon gamma(Sigma) was added to the media at a final concentration of 100 ng/ml.Cells were incubated for 8 hrs after induction. After 8 hrs, 100 uL ofSteady-Glo (Promega) was added into each well, incubated at roomtemperature for 30 min, and then read in a standard plate luminometer(Molecular Devices, Sunnyvale, Calif.). Each treatment for each reporterconstruct was assayed in triplicate, and the average of the 3 replicateswithout treatment and the average of the 3 replicates with treatmentswere recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the interferon response in this assay, and that can beused as biomarkers for the interferon response, are identified in Table1, section 6 and section 6a.

1.7 Biological Response to CREB Activation

Transient transfection assays were conducted in Hela cells (ATCC,Manassas, Va.) in 384-well white plates. First, 4,000 cells per wellwere seeded in standard culture medium for 24 hr. Next, 50 ng ofreporter plasmid DNA per well was transfected with Fugene-6 transfectionreagent (Roche Diagnostics, Indianapolis, Ind.) according to Fugenestandard protocols. After 16 hrs, the transfection medium was removedand fresh culture medium with or without the addition of an inducingcompound was added to each well. For the no treatment control, onlyfresh media was added to the wells. Inductions were done by two separatetreatments: forskolin (Sigma) (protein kinase A activator) was added tothe media at a final concentration of 20 uM, and phorbol 12-myristate13-acetate (Promega) (protein kinase C activator) was added to the mediaat a final concentration of 100 nM. Cells were incubated for 4 hrs afterinduction. After 4 hrs, 100 uL of Steady-Glo (Promega) was added intoeach well, incubated at room temperature for 30 min, and then read in astandard plate luminometer (Molecular Devices, Sunnyvale, Calif.). Eachtreatment for each reporter construct was assayed in triplicate, and theaverage of the 3 replicates without treatment and the average of the 3replicates with treatments were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the CREB activation response in this assay, and that canbe used as biomarkers for the CREB activation response, are identifiedin Table 1, section 7 and section 7a.

1.8 Biological Response to Glucocorticoid Receptor Ligands

Transient transfection assays were conducted in HT1080 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 5,000 cells per well wereseeded in standard culture medium for 24 hr. Next, 50 ng of reporterplasmid DNA was transfected with Fugene-6 transfection reagent (RocheDiagnostics, Indianapolis, Ind.) according to Fugene standard protocols.After 16 hrs, the transfection medium was removed and fresh culturemedium with or without the addition of an inducing compound was added toeach well. For the no treatment control, only fresh media was added tothe wells. Inductions were done by three separate treatments:dexamethasone (Sigma) was added to the media of the treated samples at afinal concentration of 100 nM, prednisone (Sigma) was added to the mediaof the treated samples at a final concentration of 1 uM, and cortisone(Sigma) was added to the media of the treated samples at a finalconcentration of 1 uM. Cells were incubated for 4 hrs after induction.After 4 hrs, 100 uL of Steady-Glo (Promega) was added into each well,incubated at room temperature for 30 min, and then read in a standardplate luminometer (Molecular Devices, Sunnyvale, Calif.). Each treatmentfor each reporter construct was assayed in triplicate, and the averageof the 3 replicates without treatment and the average of the 3replicates with treatment were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the glucocorticoid-mediated response in this assay, andthat can be used as biomarkers for the glucocorticoid-mediated response,are identified in Table 1, section 8 and section 8a.

1.9 Biological Response to PPAR Ligands

Transient transfection assays were conducted in HepG2 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 10,000 cells per wellwere seeded in charcoal stripped culture medium for 24 hr. Next, 100 ngof reporter plasmid DNA and 20 ng of a PPAR cDNA expression plasmid(Origene) per well were transfected with Fugene-6 transfection reagent(Roche Diagnostics, Indianapolis, Ind.) according to Fugene standardprotocols. After 16 hrs, the transfection medium was removed and freshculture medium with or without the addition of an inducing compound wasadded to each well. For the no treatment control, only fresh media wasadded to the wells. Inductions were done by three separate treatments:WY14643 (Cayman) was added to the media of the treated samples at afinal concentration of 75 uM to induce PPAR alpha, ciglitazone (Biomol)was added to the media of the treated samples at a final concentrationof 10 uM to induce PPAR gamma, and GW501516 (Alexis) was added to themedia of the treated samples at a final concentration of 100 nM toinduce PPAR delta. Cells were incubated for 24 hrs after induction.After 24 hrs, 100 uL of Steady-Glo (Promega) was added into each well,incubated at room temperature for 30 min, and then read in a standardplate luminometer (Molecular Devices, Sunnyvale, Calif.). Each treatmentfor each reporter construct was assayed in triplicate, and the averageof the 3 replicates without treatment and the average of the 3replicates with treatment were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the PPAR-mediated response in this assay, and that canbe used as biomarkers for the PPAR-mediated response, are identified inTable 1, section 9 and section 9a.

1.10 Biological Response to RAR Ligands

Transient transfection assays were conducted in HepG2 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 10,000 cells per wellwere seeded in charcoal stripped culture medium for 24 hr. Next, 100 ngof reporter plasmid DNA and 20 ng of a RAR cDNA expression plasmid(Origene) per well were transfected with Fugene-6 transfection reagent(Roche Diagnostics, Indianapolis, Ind.) according to Fugene standardprotocols. After 16 hrs, the transfection medium was removed and freshculture medium with or without the addition of an inducing compound wasadded to each well. For the no treatment control, only fresh media wasadded to the wells. Inductions were done by two separate treatments:AM-580 (Biomol) was added to the media of the treated samples at a finalconcentration of 100 nM for RAR alpha and adapalene (Biomol) was addedto the media of the treated samples at a final concentration of 100 nMfor RAR beta. Cells were incubated for 24 hrs after induction. After 24hrs, 100 uL of Steady-Glo (Promega) was added into each well, incubatedat room temperature for 30 min, and then read in a standard plateluminometer (Molecular Devices, Sunnyvale, Calif.). Each treatment foreach reporter construct was assayed in triplicate, and the average ofthe 3 replicates without treatment and the average of the 3 replicateswith treatment were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the RAR-mediated response in this assay, and that can beused as biomarkers for the RAR-mediated response, are identified inTable 1, section 10 and section 10a.

1.11 Biological Response to TNFa and NFkB Activation

Transient transfection assays were conducted in HT1080 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 5,000 cells per well wereseeded in standard culture medium for 24 hr. Next, 50 ng of reporterplasmid DNA was transfected with Fugene-6 transfection reagent (RocheDiagnostics, Indianapolis, Ind.) according to Fugene standard protocols.After 16 hrs, the transfection medium was removed and fresh culturemedium with or without the addition of an inducing compound was added toeach well. For the no treatment control, only fresh media was added tothe wells. TNFa (Abcam) was added to the media of the treated samples ata final concentration of 20 ng/ml. Cells were incubated for 8 hrs afterinduction. After 8 hrs, 100 uL of Steady-Glo (Promega) was added intoeach well, incubated at room temperature for 30 min, and then read in astandard plate luminometer (Molecular Devices, Sunnyvale, Calif.). Eachtreatment for each reporter construct was assayed in triplicate, and theaverage of the 3 replicates without treatment and the average of the 3replicates with treatment were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the TNFα-mediated response in this assay, and that canbe used as biomarkers for the TNFα-mediated response, are identified inTable 1, section 11 and section 11a.

1.12 Biological Response to Heat Shock

Transient transfection assays were conducted in HT1080 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 5,000 cells per well wereseeded in standard culture medium for 24 hr. Next, 50 ng of reporterplasmid DNA was transfected with Fugene-6 transfection reagent (RocheDiagnostics, Indianapolis, Ind.) according to Fugene standard protocols.After 16 hrs, three replicates of each transfected construct was movedto 43 degrees C., and three replicates were kept at 37 degrees C. Cellswere incubated for 8 hrs at their respective temperatures. After 8 hrs,100 uL of Steady-Glo (Promega) was added into each well, incubated atroom temperature for 30 min, and then read in a standard plateluminometer (Molecular Devices, Sunnyvale, Calif.). Each treatment foreach reporter construct was assayed in triplicate, and the average ofthe 3 replicates without treatment and the average of the 3 replicateswith treatment were recorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the heat shock response in this assay, and that can beused as biomarkers for the heat shock response, are identified in Table1, section 12 and section 12a.

1.13 Biological Response to Serum

Transient transfection assays were conducted in HT1080 cells (ATCC,Manassas, Va.) in 96-well white plates. First, 7,500 cells per well wereseeded in a starvation medium (phenol-free Opti-MEM) for 24 hr. Next, 50ng of reporter plasmid DNA per well was transfected with Fugene-6transfection reagent (Roche Diagnostics, Indianapolis, Ind.) accordingto Fugene standard protocols. After 16 hrs, the transfection medium wasremoved and fresh culture medium with or without the addition of fetalbovine serum was added to each well. For the no treatment control, onlyfresh media was added to the wells. Inductions were done by adding fetalbovine serum to the media at a final concentration of 20%. Cells wereincubated for 8 hrs after induction. After 8 hrs, 100 uL of Steady-Glo(Promega) was added into each well, incubated at room temperature for 30min, and then read in a standard plate luminometer (Molecular Devices,Sunnyvale, Calif.). Each treatment for each reporter construct wasassayed in triplicate, and the average of the 3 replicates withouttreatment and the average of the 3 replicates with treatments wererecorded.

Transcription regulatory sequences, the activity of which is highlycorrelated with the serum response in this assay, and that can be usedas biomarkers for the serum response, are identified in Table 1, section13 and section 13a.

REFERENCES

-   U.S. 2007-0161031, Jul. 12, 2007, TRINKLEIN, N. D. et al.-   U.S. 2009-0018031, Jan. 15, 2009, TRINKLEIN, N. D. et al.-   COOPER, S. J. et al., Genome Res., 2006, 16:1-10-   GUILLEM, K. et al., Cell, 1997 89:9-12-   TRINKLEIN, N. D. et al., Genome Res., 2003, 13:308-312-   TRINKLEIN, N. D. et al., Genome Res., 2004, 14:62-66

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

1. A collection comprising a plurality of expression constructs, eachexpression construct comprising a transcriptional regulatory sequenceoperatively linked with a heterologous sequence encoding a reporter,wherein at least 20% of the expression constructs in the collection eachcomprise a transcription regulatory sequence of a different gene ofTable
 1. 2. The collection of claim 1 wherein the transcriptionregulatory sequences of the different genes of Table 1 are biomarkers ofthe same biological response.
 3. The collection of claim 1 wherein thetranscription regulatory sequences of the different genes of Table 1comprise biomarkers of different biological responses.
 4. The collectionof claim 1 wherein the expression construct is comprised in a plasmid, avirus, artificial chromosome, or a transposon vector or is integratedinto a chromosome in a cell or maintained as a stable episomal vector.5. The collection of claim 1 wherein the reporter is a light-emittingreporter, a fluorescent reporter or a colorimetric reporter. 6.(canceled)
 7. A cell line comprising at least one expression constructthat is stably integrated into a chromosome or stably maintained in aepisomal vector wherein the expression construct comprises atranscriptional regulatory sequence operatively linked with aheterologous sequence encoding a reporter, wherein the expressionconstruct comprises a transcription regulatory sequence of a gene ofTable
 1. 8. (canceled)
 9. (canceled)
 10. A method comprising: a)exposing at least one cell to a test condition, wherein the at least onecell comprises at least one expression construct comprising atranscriptional regulatory sequence operatively linked with aheterologous sequence encoding a reporter, wherein the transcriptionregulatory sequence is a transcription regulatory sequence of a gene ofTable 1; b) measuring expression of the reporter; and c) correlating themeasurement with a biological response for which the transcriptionregulatory sequence is a biomarker.
 11. The method of claim 11 furthercomprising i) measuring the activity of the reporter in the absence ofthe test condition or a control condition; and ii) measuring theactivity of the reporter in the presence of the test condition; and iii)measuring the difference or ratio of reporter activity between the cellsexposed to the test condition and cells that were not; and iv)correlating the difference or ratio between treated and untreatedmeasurements with a biological response.
 12. The method of claim 11wherein the transcription regulatory sequence comprises a sequenceselected from the group consisting of: (i) any of SEQ ID NO:1 to SEQ IDNO: 174 (ii) a sequence of at least 50 nucleotides having at least 95%sequence identity to a sequence of (i) (iii) a fragment of a sequence of(i).
 13. The method of claim 11 wherein the test condition is selectedfrom the group consisting of contacting the cell with a test compound,exposing the cell to an environmental condition and inducing orrepressing expression of one or more genes in the cell.
 14. The methodof claim 11 wherein the test condition comprises contacting the cellwith a test compound selected from: (1) a small organic molecule; (2) anucleic acid derivative (e.g., a small interfering RNA, micro RNA mimicor micro RNA inhibitor); and (3) an expression construct that containsan open reading frame of a gene.
 15. The method of claim 11 wherein eachexpression construct is comprised in a different cell.
 16. The method ofclaim 11 wherein the biological responses are responses selected fromthe hypoxia response, glucocorticoid response, estrogen response,PPAR-mediated response, retinoic acid response, heat shock response,p53-mediated response, NFkB-mediated response, STAT1-mediated response,CREB-mediated response, serum response and SREBP-mediated response. 17.The method of claim 11 further comprising, if the measurement is at atarget level; i) exposing at least one second cell to the testcondition, wherein the at least one second cell comprises at least oneexpression construct comprising a transcriptional regulatory sequenceoperatively linked with a heterologous sequence encoding a reporter,wherein the transcription regulatory sequence is a transcriptionregulatory sequence of a different gene of the same biological responseof Table 1; and; ii) measuring expression of the reporter sequence inthe at least one second cell.